WO2024182295A2

WO2024182295A2 - Targeted spatial sequencing

Info

Publication number: WO2024182295A2
Application number: PCT/US2024/017299
Authority: WO
Inventors: Martin Maria FABANI; Michael Lawson
Original assignee: Singular Genomics Systems, Inc.
Priority date: 2023-02-27
Filing date: 2024-02-26
Publication date: 2024-09-06
Also published as: WO2024182295A3

Abstract

Disclosed herein, inter alia, are oligonucleotide probes, methods, and kits useful for amplifying and detecting target nucleic acids in cells and tissues.

Description

TARGETED SPATIAL SEQUENCING

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims the benefit of U.S. Provisional Application No. 63/621,418, filed January 16, 2024, and U.S. Provisional Application No. 63/487,200, filed February 27, 2023, each of which is incorporated herein by reference in their entirety and for all purposes.

BACKGROUND

[0002] DNA sequencing is a fundamental tool in biological and medical research; it is an essential technology for the paradigm of personalized precision medicine. Additionally, singlecell technologies have emerged to enable profiling the composition of the genome, epigenome, transcriptome, or proteome of a single cell. Uncovering the distribution, heterogeneity, spatial gene and protein co-expression patterns within cells and tissues is vital for understanding how cell co-localization influences tissue development and the spread of diseases such as cancer, which could lead to important new discoveries and therapeutics. Beyond quantifying gene and protein expression, obtaining precise sequencing information enables identification, monitoring, and possible treatment at the molecular level. Disclosed herein, inter alia, are solutions to these and other problems in the art.

BRIEF SUMMARY

[0003] In an aspect is provided a method of generating a complex including a circular polynucleotide in a cell, the method including: i) hybridizing a splint oligonucleotide to an extended oligonucleotide probe, thereby forming a complex, wherein the splint oligonucleotide includes a probe sequence complement and a target sequence, wherein the probe sequence complement of the splint oligonucleotide hybridizes to a probe sequence of the extended oligonucleotide probe, wherein the target sequence of the splint oligonucleotide hybridizes to a target sequence complement of the extended oligonucleotide probe, and wherein a subject sequence complement is located between the probe sequence and the target sequence complement of the extended oligonucleotide probe; ii) extending the splint oligonucleotide of the complex along the extended oligonucleotide probe with a polymerase to generate an extended splint oligonucleotide including a complement of the subject sequence; and iii) circularizing the extended splint oligonucleotide by ligating the extended splint oligonucleotide to the splint binding sequence of the oligonucleotide probe, thereby forming the complex including the circular polynucleotide. [0004] In an aspect is provided a method of generating a complex including a circular polynucleotide in a cell, the method including: a) hybridizing a splint oligonucleotide to an extended oligonucleotide probe, thereby forming a complex, wherein the splint oligonucleotide includes a probe sequence complement and a target sequence, wherein the probe sequence complement of the splint oligonucleotide hybridizes to a probe sequence of the extended oligonucleotide probe, wherein the target sequence of the splint oligonucleotide hybridizes to a target sequence complement of the extended oligonucleotide probe, and wherein a subject sequence complement is located between the probe sequence and the target sequence complement of the extended oligonucleotide probe; b) contacting the complex with an exonuclease enzyme and generating an extended oligonucleotide probe including a 3’ end, wherein the exonuclease enzyme removes a single-stranded portion of the complex; and c) ligating the probe sequence to the 3’ end of the extended oligonucleotide probe, thereby generating a complex including a circular oligonucleotide.

[0005] In an aspect is provided a complex including: i) a circular polynucleotide including a probe sequence, a target hybridization sequence, a subject sequence complement, and a target sequence complement; and ii) a splint oligonucleotide hybridized to the circular polynucleotide, wherein the splint oligonucleotide includes a probe sequence complement hybridized to the probe sequence of the circular polynucleotide, and wherein the splint oligonucleotide includes a target sequence hybridized to the target sequence complement of the circular polynucleotide.

[0006] In an aspect is provided a kit including: a) an oligonucleotide probe including a target hybridization sequence and a probe sequence, wherein the target hybridization sequence is complementary to a probe hybridization sequence in a target polynucleotide; and b) a splint oligonucleotide including a target sequence and a probe sequence complement, wherein the target sequence is substantially identical to a sequence in the target polynucleotide, and wherein the probe sequence complement is capable of hybridizing to the probe sequence of the oligonucleotide probe.

BRIEF DESCRIPTION OF THE DRAWINGS

[0007] FIGS. 1 A-1H are a series of cartoon depictions of a cell that is attached to a substrate surface and fixed (e.g., using a fixing agent) and permeabilized according to known methods. The cell may have been cultured on the surface, or the cell may have been initially cultured in suspension and then fixed to the surface. According to the methods and compositions described herein, the nucleic acid (e.g., mRNAs) present in the cell (depicted as a wavy line, wherein Ml, M2, and M3 represent different mRNA species) are subjected to an amplification technique where a targeted oligonucleotide primer (i.e., target oligonucleotide probe) anneals to the nucleic acid, for example, the mRNA species labeled M2. The target oligonucleotide hybridizes to the mRNA molecule at a region downstream (i.e., an adjacent region in the 3’ direction) of the subject sequence (FIG. 1 A). As shown in FIG. IB, the hybridized oligonucleotide probe is then extended with a polymerase (e.g., a strand-displacing reverse transcriptase, shown as a cloud-like object) to generate a cDNA copy of the target nucleic acid including the subject sequence. The cellular RNA may then be digested (e.g., digested with a ribonuclease, such as RNAse H), and a splint oligonucleotide including regions of complementarity to the oligonucleotide probe and cDNA is hybridized to the extended oligonucleotide probe, as shown in FIG. 1C. The dashed lines are meant to guide the eye to the hybridization sites. As shown in FIG. ID, the 3’ overhang of the extended oligonucleotide probe (i.e., a 3’ tail sequence of the extended oligonucleotide probe including cDNA that is not complementary to the splint oligonucleotide) may then be digested (e.g., digested with a single-stranded 3’ exonuclease), and the extended oligonucleotide probe is ligated (not shown) to form a circular polynucleotide. The resulting circular polynucleotide may be primed, e.g., with the 3’ end of the splint oligonucleotide and extended with a strand-displacing polymerase to generate a concatemer containing multiple copies of the subject sequence, as depicted in FIG. IE. Alternatively, following hybridization of the splint oligonucleotide to the extended oligonucleotide probe, the 3’ end of the splint oligonucleotide is extended with a polymerase (e.g., a non strand-displacing polymerase) and ligated to form a circular polynucleotide, as shown in FIG. IF. As shown in FIG. 1G, the 3’ overhang of the extended oligonucleotide probe (i.e., a 3’ tail sequence of the extended oligonucleotide probe including cDNA that is not complementary to the splint oligonucleotide) is then digested (e.g., digested with a single-stranded 3’ exonuclease), generating a 3’ end in the extended oligonucleotide probe. The circular polynucleotide may be primed, e.g., with the 3’ end of the extended oligonucleotide probe and extended with a strand-displacing polymerase to generate a concatemer containing multiple copies of the subject sequence, as depicted in FIG. 1H. It is understood that for convenience, the cell, enzymes, and nucleic acid molecules are enlarged and are not to scale.

[0008] FIGS. 2A-2C illustrate embodiments of the oligonucleotide probes described herein. FIG. 2A illustrates the targeting oligonucleotide primer (i.e., the target oligonucleotide probe) as a single-stranded oligonucleotide containing a target hybridization sequence at a 3’ end (i.e., a sequence complementary to a probe hybridization sequence in a target nucleic acid), and a probe sequence. In some embodiments, the probe sequence includes one or more primer binding sequences. In embodiments, the probe sequence includes a nucleic acid sequence complementary to a splint oligonucleotide. In embodiments, the probe sequence includes a first primer binding sequence complementary to a first amplification primer (e.g., a rolling circle amplification primer), and a second primer binding sequence complementary to a second amplification primer. In embodiments, the first primer binding sequence includes a nucleic acid sequence complementary to the second amplification primer, and the second primer binding sequence includes a nucleic acid sequence complementary to the first amplification primer. FIGS. 2B and 2C illustrate embodiments of a splint oligonucleotide, wherein each embodiment includes a target sequence at a 3’ end and a probe sequence complement (e.g., a sequence complementary to the probe sequence of the oligonucleotide probe) at a 5’ end, and wherein the embodiment in FIG. 2C includes a spacer sequence (e.g., a 5 to 15 nucleotide sequence) between the target sequence and the probe sequence complement. In embodiments, the target sequence of the splint oligonucleotide may include a sequence that is substantially the same as a sequence of the target nucleic acid, or may include a sequence that is capable of hybridizing to the complement of a sequence of the target nucleic acid.

[0009] FIGS. 3A-3H illustrate embodiments of the methods described herein for amplifying and sequencing a target nucleic acid. FIG. 3 A illustrates hybridizing a target oligonucleotide probe to a target nucleic acid sequence (e.g., a probe hybridization sequence of an mRNA molecule), wherein the target hybridization sequence is located at a 3’ end of the target oligonucleotide probe. The probe hybridization sequence is located downstream (i.e., in the 3’ direction) of a subject sequence (e.g., a subject sequence of the mRNA molecule that includes the sequence information of interest for downstream assays, such as in in situ sequencing). Upstream (i.e., in the 5’ direction) of the subject sequence is the target sequence. Following hybridization of the oligonucleotide probe, the 3’ end is extended with, e.g., a strand-displacing reverse transcriptase such as M-MLV or SSIV RT, to generate an extended oligonucleotide probe including a copy of the subject sequence (i.e., a subject sequence complement) and target sequence (i.e., a target sequence complement). In some embodiments, additional sequence(s) upstream of the target sequence (referred to herein as a “tail sequence”) are also incorporated into the extended oligonucleotide probe. RNA digestion, e.g., with a ribonuclease such as RNAse H, may be performed to remove the target mRNA, leaving behind the extended oligonucleotide probe with a 3’ end, as shown in FIG. 3B. In embodiments, a splint oligonucleotide as illustrated in FIGS. 2B or 2C is then hybridized to the extended oligonucleotide probe as illustrated in FIG. 3C, wherein the probe sequence complement at the 5’ end of the splint oligonucleotide is hybridized to the probe sequence at the 5’ end of the extended oligonucleotide probe, and the target sequence at the 3’ end of the splint oligo is hybridized to the target sequence complement of the extended oligonucleotide primer. In embodiments, a 3’ overhang of the extended oligonucleotide probe (e.g., the tail sequence complement) is generated following hybridization of the splint oligonucleotide due to the presence of non-complementary sequence. Exonuclease digestion of the tail sequence complement using a single-stranded 3 ’-5’ exonuclease (e.g., Exonuclease I; shown as a circular partition) is then performed, as shown in FIG. 3D, digesting the 3’ overhang region of the extended oligonucleotide probe. The 5’ end and 3’ end of the extended oligonucleotide probe are then ligated (e.g., ligated with T4 DNA ligase) to generate a circular polynucleotide. Using the splint oligonucleotide as an amplification primer, rolling circle amplification may be performed with a strand-displacing polymerase (e.g., a phi29 polymerase, shown as a cloud-like object) to generate a concatemer including multiple copies of the subject sequence, for example, as shown in FIG. 3E. Additional amplification primers may be hybridized to the amplification product (e.g., to one or more primer binding sequences, or complements thereof) of FIG. 3E and extended, thereby generating additional amplification products. Shown in FIG. 3F is an alternate embodiment to generate a circular polynucleotide, wherein after hybridizing the splint oligonucleotide (e.g., the splint oligo illustrated in FIG. 2C) to the extended oligonucleotide probe, the 3’ end of the splint oligonucleotide is extended using a non-strand displacing polymerase (e.g., T4 DNA polymerase, illustrated as a cloud-like object), generating an extended splint oligonucleotide including the subject sequence, probe hybridization sequence, and probe sequence complement. The 5’ and 3’ ends of the extended splint oligonucleotide are then ligated (e.g., ligated with T4 DNA ligase) to form a circularized polynucleotide. Exonuclease digestion of the tail sequence complement using a single-stranded 3’-5’ exonuclease (e.g., Exonuclease I; shown as a circular partition) is then performed, as shown in FIG. 3G, digesting the 3’ overhang region of the extended oligonucleotide probe and generating a 3’ end (i.e., a 3’ end duplex with the circular polynucleotide). The duplexed 3’ end of the extended oligonucleotide probe may then be used as an amplification primer for rolling circle amplification with a strand displacing polymerase (e.g., a phi29 polymerase, illustrated as a cloud-like object), generating a concatemer including multiple copies of the subject sequence complement, for example.

Additional amplification primers may be hybridized to the amplification product (e.g., to one or more primer binding sequences, or complements thereof) of FIG. 3G and extended, thereby generating additional amplification products. As an alternate embodiment to the process illustrated in FIG. 3G, an amplification primer with complementarity to the splint oligonucleotide sequence, for example, may be hybridized directly to the circular polynucleotide and extended, as shown in FIG. 3H.

[0010] FIG. 4 is a set of fluorescence microscopy images of in situ transcript sequencing through three cycles performed in one well of a 96-well plate in Ramos Burkitt’s lymphoma cells. The method described and illustrated in FIGS. 3 A-3E were used to generate the sequencing signals for FIG. 4. The sequencing primer used is complementary to a sequence of the subject sequence. The small dots present in all of the images are focusing beads. The circles are used to guide the eye and highlight the location of the detected signal for each sequencing cycle, wherein the sequence ‘TCC’ was detected.

[0011] FIG. 5 is a set of fluorescence microscopy images of in situ transcript sequencing through three cycles performed in one well of a 96-well plate in Ramos Burkitt’s lymphoma cells. The method illustrated in FIGS. 3 A-3C and 3F-3G were used to generate the sequencing signal. The sequencing primer used is complementary to a sequence of the subject sequence. The circles are used to guide the eye and highlight the location of the detected signal for each sequencing cycle, wherein the sequence ‘ AGT’ was detected.

DETAILED DESCRIPTION

[0012] The aspects and embodiments described herein relate to systems and methods for analyzing a cell and cellular components (e.g., RNA transcripts, proteins, or analytes). Data obtained from the proteome and transcriptome is used in research to gain insight into processes such as cellular differentiation, carcinogenesis, transcription regulation, and biomarker discovery, among others. The methods provide significant advantages in terms of speed and detection efficiency of target polynucleotides, and may be performed on solid supports or in cells or tissue sections in situ.

I. Definitions

[0013] All patents, patent applications, articles and publications mentioned herein, both supra and infra, are hereby expressly incorporated herein by reference in their entireties. The practice of the technology described herein will employ, unless indicated specifically to the contrary, conventional methods of chemistry, biochemistry, organic chemistry, molecular biology, bioinformatics, microbiology, recombinant DNA techniques, genetics, immunology, and cell biology that are within the skill of the art, many of which are described below for the purpose of illustration. Examples of such techniques are available in the literature. See, e.g., Singleton et al., DICTIONARY OF MICROBIOLOGY AND MOLECULAR BIOLOGY 2nd ed., J. Wiley & Sons (New York, NY 1994); and Sambrook and Green, Molecular Cloning: A Laboratory Manual, 4th Edition (2012). Methods, devices and materials similar or equivalent to those described herein can be used in the practice of this invention.

[0014] Unless defined otherwise herein, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. Various scientific dictionaries that include the terms included herein are well known and available to those in the art. Although any methods and materials similar or equivalent to those described herein find use in the practice or testing of the disclosure, some preferred methods and materials are described. Accordingly, the terms defined immediately below are more fully described by reference to the specification as a whole. It is to be understood that this disclosure is not limited to the particular methodology, protocols, and reagents described, as these may vary, depending upon the context in which they are used by those of skill in the art. The following definitions are provided to facilitate understanding of certain terms used frequently herein and are not meant to limit the scope of the present disclosure.

[0015] As used herein, the singular terms “a”, “an”, and “the” include the plural reference unless the context clearly indicates otherwise. Reference throughout this specification to, for example, "one embodiment", "an embodiment", "another embodiment", "a particular embodiment", "a related embodiment", "a certain embodiment", "an additional embodiment", or "a further embodiment" or combinations thereof means that a particular feature, structure or characteristic described in connection with the embodiment is included in at least one embodiment of the present disclosure. Thus, the appearances of the foregoing phrases in various places throughout this specification are not necessarily all referring to the same embodiment. Furthermore, the particular features, structures, or characteristics may be combined in any suitable manner in one or more embodiments.

[0016] As used herein, the term “about” means a range of values including the specified value, which a person of ordinary skill in the art would consider reasonably similar to the specified value. In embodiments, the term “about” means within a standard deviation using measurements generally acceptable in the art. In embodiments, about means a range extending to +/- 10% of the specified value. In embodiments, about means the specified value.

[0017] Throughout this specification, unless the context requires otherwise, the words “comprise”, “comprises” and “comprising” will be understood to imply the inclusion of a stated step or element or group of steps or elements but not the exclusion of any other step or element or group of steps or elements. By “consisting of’ is meant including, and limited to, whatever follows the phrase “consisting of.” Thus, the phrase “consisting of’ indicates that the listed elements are required or mandatory, and that no other elements may be present. By “consisting essentially of’ is meant including any elements listed after the phrase, and limited to other elements that do not interfere with or contribute to the activity or action specified in the disclosure for the listed elements. Thus, the phrase “consisting essentially of’ indicates that the listed elements are required or mandatory, but that other elements are optional and may or may not be present depending upon whether or not they affect the activity or action of the listed elements.

[0018] As used herein, the term “control” or “control experiment” is used in accordance with its plain and ordinary meaning and refers to an experiment in which the subjects or reagents of the experiment are treated as in a parallel experiment except for omission of a procedure, reagent, or variable of the experiment. In some instances, the control is used as a standard of comparison in evaluating experimental effects.

[0019] As used herein, the term “complement” is used in accordance with its plain and ordinary meaning and refers to a nucleotide (e.g., RNA nucleotide or DNA nucleotide) or a sequence of nucleotides capable of base pairing with a complementary nucleotide or sequence of nucleotides (e.g., Watson-Crick base pairing). As described herein and commonly known in the art the complementary (matching) nucleotide of adenosine is thymidine and the complementary (matching) nucleotide of guanosine is cytosine. Thus, a complement may include a sequence of nucleotides that base paired with corresponding complementary nucleotides of a second nucleic acid sequence. The nucleotides of a complement may partially or completely match the nucleotides of the second nucleic acid sequence. Where the nucleotides of the complement completely match each nucleotide of the second nucleic acid sequence, the complement forms base pairs with each nucleotide of the second nucleic acid sequence. Where the nucleotides of the complement partially match the nucleotides of the second nucleic acid sequence only some of the nucleotides of the complement form base pairs with nucleotides of the second nucleic acid sequence. Examples of complementary sequences include coding and non-coding sequences, wherein the non-coding sequence contains complementary nucleotides to the coding sequence and thus forms the complement of the coding sequence. A further example of complementary sequences are sense and antisense sequences, wherein the sense sequence contains complementary nucleotides to the antisense sequence and thus forms the complement of the antisense sequence. Another example of complementary sequences are a template sequence and an amplicon sequence polymerized by a polymerase along the template sequence. “Duplex” means at least two oligonucleotides and/or polynucleotides that are fully or partially complementary undergo Watson-Crick type base pairing among all or most of their nucleotides so that a stable complex is formed. Complementary single stranded nucleic acids and/or substantially complementary single stranded nucleic acids can hybridize to each other under hybridization conditions, thereby forming a nucleic acid that is partially or fully double stranded. When referring to a double-stranded polynucleotide including a first strand hybridized to a second strand, it is understood that each of the first strand and the second strand are independently single- stranded polynucleotides. All or a portion of a nucleic acid sequence may be substantially complementary to another nucleic acid sequence, in some embodiments. As referred to herein, “substantially complementary” refers to nucleotide sequences that can hybridize with each other under suitable hybridization conditions. Hybridization conditions can be altered to tolerate varying amounts of sequence mismatch within complementary nucleic acids that are substantially complementary. Substantially complementary portions of nucleic acids that can hybridize to each other can be 75% or more, 76% or more, 77% or more, 78% or more, 79% or more, 80% or more, 81% or more, 82% or more, 83% or more, 84% or more, 85% or more, 86% or more, 87% or more, 88% or more, 89% or more, 90% or more, 91% or more, 92% or more, 93% or more, 94% or more, 95% or more, 96% or more, 97% or more, 98% or more or 99% or more complementary to each other. In some embodiments substantially complementary portions of nucleic acids that can hybridize to each other are 100% complementary. Nucleic acids, or portions thereof, that are configured to hybridize to each other often include nucleic acid sequences that are substantially complementary to each other.

[0020] As described herein, the complementarity of sequences may be partial, in which only some of the nucleic acids match according to base pairing, or complete, where all the nucleic acids match according to base pairing. Thus, two sequences that are complementary to each other, may have a specified percentage of nucleotides that complement one another (e.g., about 60%, preferably 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher complementarity over a specified region). In embodiments, two sequences are complementary when they are completely complementary, having 100% complementarity. In embodiments, sequences in a pair of complementary sequences form portions of a single polynucleotide with non-base-pairing nucleotides (e.g., as in a hairpin or loop structure, with or without an overhang) or portions of separate polynucleotides. In embodiments, one or both sequences in a pair of complementary sequences form portions of longer polynucleotides, which may or may not include additional regions of complementarity.

[0021] As used herein, the term “contacting” is used in accordance with its plain ordinary meaning and refers to the process of allowing at least two distinct species (e.g., chemical compounds including biomolecules, particles, solid supports, or cells) to become sufficiently proximal to react, interact or physically touch. It should be appreciated, however, that the resulting reaction product can be produced directly from a reaction between the added reagents or from an intermediate from one or more of the added reagents which can be produced in the reaction mixture. The term “contacting” may include allowing two species to react, interact, or physically touch, wherein the two species may be a compound as described herein and a protein or enzyme.

[0022] As may be used herein, the terms “nucleic acid,” “nucleic acid molecule,” “nucleic acid sequence,” “strand,” “nucleic acid fragment” and “polynucleotide” are used interchangeably and are intended to include, but are not limited to, a polymeric form of nucleotides covalently linked together that may have various lengths, either deoxyribonucleotides or ribonucleotides, or analogs, derivatives or modifications thereof. Different polynucleotides may have different three- dimensional structures, and may perform various functions, known or unknown. Non-limiting examples of polynucleotides include a gene, a gene fragment, an exon, an intron, intergenic DNA (including, without limitation, heterochromatic DNA), messenger RNA (mRNA), transfer RNA, ribosomal RNA, a ribozyme, cDNA, a recombinant polynucleotide, a branched polynucleotide, a plasmid, a vector, isolated DNA of a sequence, isolated RNA of a sequence, a nucleic acid probe, and a primer. Polynucleotides useful in the methods of the disclosure may include natural nucleic acid sequences and variants thereof, artificial nucleic acid sequences, or a combination of such sequences. As may be used herein, the terms “nucleic acid oligomer” and “oligonucleotide” are used interchangeably and are intended to include, but are not limited to, nucleic acids having a length of 200 nucleotides or less. In some embodiments, an oligonucleotide is a nucleic acid having a length of 2 to 200 nucleotides, 2 to 150 nucleotides, 5 to 150 nucleotides or 5 to 100 nucleotides. The terms “polynucleotide,” “oligonucleotide,” “oligo” or the like refer, in the usual and customary sense, to a linear sequence of nucleotides. Oligonucleotides are typically from about 5, 6, 7, 8, 9, 10, 12, 15, 25, 30, 40, 50 or more nucleotides in length, up to about 100 nucleotides in length. In some embodiments, an oligonucleotide is a primer configured for extension by a polymerase when the primer is annealed completely or partially to a complementary nucleic acid template. A primer is often a single stranded nucleic acid. In certain embodiments, a primer, or portion thereof, is substantially complementary to a portion of an adapter. In some embodiments, a primer has a length of 200 nucleotides or less. In certain embodiments, a primer has a length of 10 to 150 nucleotides, 15 to 150 nucleotides, 5 to 100 nucleotides, 5 to 50 nucleotides or 10 to 50 nucleotides. In some embodiments, an oligonucleotide may be immobilized to a solid support. In some embodiments, a polynucleotide may be a circular polynucleotide. The terms “circular polynucleotide” or “circular oligonucleotide” refer to a contiguous polynucleotide lacking a free 5’ and a free 3’ end.

[0023] As used herein, the terms “polynucleotide primer” and “primer” refers to any polynucleotide molecule that may hybridize to a polynucleotide template, be bound by a polymerase, and be extended in a template-directed process for nucleic acid synthesis (e.g., amplification and/or sequencing). The primer may be a separate polynucleotide from the polynucleotide template, or both may be portions of the same polynucleotide (e.g., as in a hairpin structure having a 3’ end that is extended along another portion of the polynucleotide to extend a double-stranded portion of the hairpin). Primers (e.g., forward or reverse primers) may be attached to a solid support. A primer can be of any length depending on the particular technique it will be used for. For example, PCR primers are generally between 10 and 40 nucleotides in length. The length and complexity of the nucleic acid fixed onto the nucleic acid template may vary. In some embodiments, a primer has a length of 200 nucleotides or less. In certain embodiments, a primer has a length of 10 to 150 nucleotides, 15 to 150 nucleotides, 5 to 100 nucleotides, 5 to 50 nucleotides or 10 to 50 nucleotides. In certain embodiments, a primer has a length of 10 to 150 nucleotides, 15 to 150 nucleotides, 5 to 100 nucleotides, 5 to 50 nucleotides or 10 to 50 nucleotides. A primer typically has a length of 10 to 50 nucleotides. For example, a primer may have a length of 10 to 40, 10 to 30, 10 to 20, 25 to 50, 15 to 40, 15 to 30, 20 to 50, 20 to 40, or 20 to 30 nucleotides. In some embodiments, a primer has a length of 18 to 24 nucleotides. One of skill can adjust these factors to provide optimum hybridization and signal production for a given hybridization procedure. The primer permits the addition of a nucleotide residue thereto, or oligonucleotide or polynucleotide synthesis therefrom, under suitable conditions. In an embodiment the primer is a DNA primer, i.e., a primer consisting of, or largely consisting of, deoxyribonucleotide residues. The primers are designed to have a sequence that is the complement of a region of template/target DNA to which the primer hybridizes. The addition of a nucleotide residue to the 3’ end of a primer by formation of a phosphodiester bond results in a DNA extension product. The addition of a nucleotide residue to the 3’ end of the DNA extension product by formation of a phosphodiester bond results in a further DNA extension product. In another embodiment the primer is an RNA primer. In embodiments, a primer is hybridized to a target polynucleotide. A “primer” is complementary to a polynucleotide template, and complexes by hydrogen bonding or hybridization with the template to give a primer/template complex for initiation of synthesis by a polymerase, which is extended by the addition of covalently bonded bases linked at its 3' end complementary to the template in the process of DNA synthesis. A “splint oligonucleotide” is used in accordance with its plain and ordinary meaning and refers to an oligonucleotide having 2 or more sequences complementary to two or more portions of a polynucleotide. An “oligonucleotide probe” or “oligonucleotide primer”, as used herein, refers to a primer including a sequence (e.g., a target hybridization sequence) at a 3’ end complementary to a sequence (e.g., a probe hybridization sequence) of a target polynucleotide (e.g., a target mRNA molecule). In embodiments, the oligonucleotide probe includes one or more sequences located 5’ (i.e., upstream) of the target hybridization sequence, for example, one or more primer binding sequences. An “extended oligonucleotide probe” or “extended oligonucleotide primer”, as used herein, referes to an oligonucleotide probe that has had one or more nucleotides incorporated into the 3’ end by a polymerase, for example, a reverse transcriptase. In embodiments, an extended oligonucleotide probe includes a region of cDNA (e.g., a cDNA sequence complemementary to a portion of an mRNA molecule) located 3’ (i.e., downstream) of the target hybridization sequence. A “target hybridization sequence” as used herein refers to a sequence at a 3’ end of an oligonucleotide probe that is complementary to a sequence in a target polynucleotide (e.g., complementary to a probe hybridization sequence of the target polynucleotide).

[0024] As used herein, the term “primer binding sequence” refers to a polynucleotide sequence that is complementary to at least a portion of a primer (e.g., a sequencing primer or an amplification primer). Primer binding sequences can be of any suitable length. In embodiments, a primer binding sequence is about or at least about 10, 15, 20, 25, 30, or more nucleotides in length. In embodiments, a primer binding sequence is 10-50, 15-30, or 20-25 nucleotides in length. The primer binding sequence may be selected such that the primer (e.g., sequencing primer) has the preferred characteristics to minimize secondary structure formation or minimize non-specific amplification, for example having a length of about 20-30 nucleotides; approximately 50% GC content, and a Tm of about 55°C to about 65°C.

[0025] Nucleic acids, including e.g., nucleic acids with a phosphorothioate backbone, can include one or more reactive moieties. As used herein, the term reactive moiety includes any group capable of reacting with another molecule, e.g., a nucleic acid or polypeptide through covalent, non-covalent or other interactions. By way of example, the nucleic acid can include an amino acid reactive moiety that reacts with an amio acid on a protein or polypeptide through a covalent, non-covalent or other interaction.

[0026] As used herein, a platform primer is a primer oligonucleotide immobilized or otherwise bound to a solid support (i.e. an immobilized oligonucleotide). Examples of platform primers include P7 and P5 primers, or S 1 and S2 sequences, or the reverse complements thereof. A “platform primer binding sequence” refers to a sequence or portion of an oligonucleotide that is capable of binding to a platform primer (e.g., the platform primer binding sequence is complementary to the platform primer). In embodiments, a platform primer binding sequence may form part of an adapter. In embodiments, a platform primer binding sequence is complementary to a platform primer sequence. In embodiments, a platform primer binding sequence is complementary to a primer. [0027] The order of elements within a nucleic acid molecule is typically described herein from 5' to 3'. In the case of a double-stranded molecule, the “top” strand is typically shown from 5' to 3', according to convention, and the order of elements is described herein with reference to the top strand.

[0028] The term “messenger RNA” or “mRNA” refers to an RNA that is without introns and is capable of being translated into a polypeptide. The term “RNA” refers to any ribonucleic acid, including but not limited to mRNA, tRNA (transfer RNA), rRNA (ribosomal RNA), and/or noncoding RNA (such as IncRNA (long noncoding RNA)). The term “cDNA” refers to a DNA that is complementary or identical to an RNA, in either single stranded or double stranded form.

[0029] A polynucleotide is typically composed of a specific sequence of four nucleotide bases: adenine (A); cytosine (C); guanine (G); and thymine (T) (uracil (U) for thymine (T) when the polynucleotide is RNA). Thus, the term “polynucleotide sequence” is the alphabetical representation of a polynucleotide molecule; alternatively, the term may be applied to the polynucleotide molecule itself. This alphabetical representation can be input into databases in a computer having a central processing unit and used for bioinformatics applications such as functional genomics and homology searching. Polynucleotides may optionally include one or more non-standard nucleotide(s), nucleotide analog(s) and/or modified nucleotides.

[0030] As used herein, the term "associated" or "associated with" can mean that two or more species are identifiable as being co-located at a point in time. An association can mean that two or more species are or were within a similar container. An association can be an informatics association, where for example digital information regarding two or more species is stored and can be used to determine that one or more of the species were co-located at a point in time. An association can also be a physical association. In some instances two or more associated species are "tethered", "coated”, "attached", or "immobilized" to one another or to a common solid or semisolid support (e.g. a receiving substrate). An association may refer to a relationship, or connection, between two entities. For example, a barcode sequence may be associated with a particular target by binding a probe including the barcode sequence to the target. In embodiments, detecting the associated barcode provides detection of the target. Associated may refer to the relationship between a sample and the DNA molecules, RNA molecules, or polynucleotides originating from or derived from that sample. These relationships may be encoded in oligonucleotide barcodes, as described herein. A polynucleotide is associated with a sample if it is an endogenous polynucleotide, i.e., it occurs in the sample at the time the sample is obtained, or is derived from an endogenous polynucleotide. For example, the RNAs endogenous to a cell are associated with that cell. cDNAs resulting from reverse transcription of these RNAs, and DNA amplicons resulting from PCR amplification of the cDNAs, contain the sequences of the RNAs and are also associated with the cell. The polynucleotides associated with a sample need not be located or synthesized in the sample, and are considered associated with the sample even after the sample has been destroyed (for example, after a cell has been lysed). Barcoding can be used to determine which polynucleotides in a mixture are associated with a particular sample. In embodiments, a proximity probe is associated with a particular barcode, such that identifying the barcode identifies the probe with which it is associated. Because the proximity probe specifically binds to a target, identifying the barcode thus identifies the target.

[0031] The term “adapter” as used herein refers to any oligonucleotide that can be ligated to a nucleic acid molecule, thereby generating nucleic acid products that can be sequenced on a sequencing platform (e.g., an Illumina or Singular Genomics G4™ sequencing platform). In embodiments, adapters include two reverse complementary oligonucleotides forming a doublestranded structure. In embodiments, an adapter includes two oligonucleotides that are complementary at one portion and mismatched at another portion, forming a Y-shaped or forkshaped adapter that is double stranded at the complementary portion and has two overhangs at the mismatched portion. Since Y-shaped adapters have a complementary, double-stranded region, they can be considered a special form of double-stranded adapters. When this disclosure contrasts Y-shaped adapters and double stranded adapters, the term “double-stranded adapter” or “blunt- ended” is used to refer to an adapter having two strands that are fully complementary, substantially (e.g., more than 90% or 95%) complementary, or partially complementary. In embodiments, adapters include sequences that bind to sequencing primers. In embodiments, adapters include sequences that bind to immobilized oligonucleotides (e.g., P7 and P5 sequences) or reverse complements thereof. In embodiments, the adapter is substantially non-complementary to the 3' end or the 5' end of any target polynucleotide present in the sample. In embodiments, the adapter can include a sequence that is substantially identical, or substantially complementary, to at least a portion of a primer, for example a universal primer. In embodiments, the adapter can include an index sequence (also referred to as barcode or tag) to assist with downstream error correction, identification or sequencing.

[0032] As used herein, the term “hairpin adapter” refers to a polynucleotide including a doublestranded stem portion and a single-stranded hairpin loop portion. In some embodiments, an adapter is hairpin adapter (also referred to herein as a hairpin). In some embodiments, a hairpin adapter includes a single nucleic acid strand including a stem-loop structure. In some embodiments, a hairpin adapter includes a nucleic acid having a 5 ’-end, a 5 ’-portion, a loop, a 3’- portion and a 3’-end (e.g., arranged in a 5’ to 3’ orientation). In some embodiments, the 5’ portion of a hairpin adapter is annealed and/or hybridized to the 3’ portion of the hairpin adapter, thereby forming a stem portion of the hairpin adapter. In some embodiments, the 5’ portion of a hairpin adapter is substantially complementary to the 3’ portion of the hairpin adapter. In certain embodiments, a hairpin adapter includes a stem portion (i.e., stem) and a loop, wherein the stem portion is substantially double stranded thereby forming a duplex. In some embodiments, the loop of a hairpin adapter includes a nucleic acid strand that is not complementary (e.g., not substantially complementary) to itself or to any other portion of the hairpin adapter. In some embodiments, a method herein includes ligating a first adapter to a first end of a double stranded nucleic acid, and ligating a second adapter to a second end of a double stranded nucleic acid. In some embodiments, the first adapter and the second adapter are different. For example, in certain embodiments, the first adapter and the second adapter may include different nucleic acid sequences or different structures. In some embodiments, the first adapter is a Y-adapter and the second adapter is a hairpin adapter. In some embodiments, the first adapter is a hairpin adapter and a second adapter is a hairpin adapter. In certain embodiments, the first adapter and the second adapter may include different primer binding sites, different structures, and/or different capture sequences (e.g., a sequence complementary to a capture nucleic acid). In some embodiments, some, all or substantially all of the nucleic acid sequence of a first adapter and a second adapter are the same. In some embodiments, some, all or substantially all of the nucleic acid sequence of a first adapter and a second adapter are substantially different.

[0033] As used herein, the terms “analogue” and “analog”, in reference to a chemical compound, refers to compound having a structure similar to that of another one, but differing from it in respect of one or more different atoms, functional groups, or substructures that are replaced with one or more other atoms, functional groups, or substructures. In the context of a nucleotide, a nucleotide analog refers to a compound that, like the nucleotide of which it is an analog, can be incorporated into a nucleic acid molecule e.g., an extension product) by a suitable polymerase, for example, a DNA polymerase in the context of a nucleotide analogue. The terms also encompass nucleic acids containing known nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, or non-naturally occurring, which have similar binding properties as the reference nucleic acid, and which are metabolized in a manner similar to the reference nucleotides. Examples of such analogs include, without limitation, phosphodiester derivatives including, e.g., phosphoramidate, phosphorodiamidate, phosphorothioate (also known as phosphorothioate having double bonded sulfur replacing oxygen in the phosphate), phosphorodithioate, phosphonocarboxylic acids, phosphonocarboxylates, phosphonoacetic acid, phosphonoformic acid, methyl phosphonate, boron phosphonate, or O- methylphosphoroamidite linkages (see, e.g., see Eckstein, OLIGONUCLEOTIDES AND ANALOGUES: A PRACTICAL APPROACH, Oxford University Press) as well as modifications to the nucleotide bases such as in 5-methyl cytidine or pseudouridine; and peptide nucleic acid backbones and linkages. Other analog nucleic acids include those with positive backbones; non-ionic backbones, modified sugars, and non-ribose backbones (e.g. phosphorodiamidate morpholino oligos or locked nucleic acids (LNA)), including those described in U.S. Patent Nos. 5,235,033 and 5,034,506, and Chapters 6 and 7, ASC Symposium Series 580, CARBOHYDRATE MODIFICATIONS IN ANTISENSE RESEARCH, Sanghui & Cook, eds. Nucleic acids containing one or more carbocyclic sugars are also included within one definition of nucleic acids. Modifications of the ribose-phosphate backbone may be done for a variety of reasons, e.g, to increase the stability and half-life of such molecules in physiological environments or as probes on a biochip. Mixtures of naturally occurring nucleic acids and analogs can be made; alternatively, mixtures of different nucleic acid analogs, and mixtures of naturally occurring nucleic acids and analogs may be made. In embodiments, the internucleotide linkages in DNA are phosphodiester, phosphodiester derivatives, or a combination of both.

[0034] Other analog nucleic acids include bis-locked nucleic acids (bisLNAs; e.g., including those described in Moreno PMD et al. Nucleic Acids Res. 2013; 41(5):3257-73), twisted intercalating nucleic acids (TINAs; e.g., including those described in Doluca O et al. Chembiochem. 2011; 12(15):2365-74), bridged nucleic acids (BNAs; e.g., including those described in Soler-Bistue A et al. Molecules. 2019; 24(12): 2297), 2’-O-methyl RNA:DNA chimeric nucleic acids (e.g., including those described in Wang S and Kool ET. Nucleic Acids Res. 1995; 23(7): 1157-1164), minor groove binder (MGB) nucleic acids (e.g., including those described in Kutyavin IV et al. Nucleic Acids Res. 2000; 28(2):655-61), morpholino nucleic acids (e.g., including those described in Summerton J and Weller D. Antisense Nucleic Acid Drug Dev. 1997; 7(3): 187-95), C5-modified pyrimidine nucleic acids (e.g., including those described in Kumar P et al. J. Org. Chem. 2014; 79(11): 5047-5061), peptide nucleic acids (PNAs; e.g., including those described in Gupta A et al. J. Biotechnol. 2017; 259: 148-59), and/or phosphorothioate nucleotides (e.g., including those described in Eckstein F. Nucleic Acid Ther. 2014; 24(6):374-87).

[0035] As used herein, a “native” nucleotide is used in accordance with its plain and ordinary meaning and refers to a naturally occurring nucleotide that does not include an exogenous label (e.g., a fluorescent dye, or other label) or chemical modification such as may characterize a nucleotide analog. Examples of native nucleotides useful for carrying out procedures described herein include: dATP (2 eoxyadenosine-5’ -triphosphate); dGTP (2’-deoxyguanosine-5’- triphosphate); dCTP (2’ -deoxy cytidine-5’ -triphosphate); dTTP (2’-deoxythymidine-5’- triphosphate); and dUTP (2’-deoxyuridine-5’-triphosphate).

[0036] In embodiments, the nucleotides of the present disclosure use a cleavable linker to attach the label to the nucleotide. The use of a cleavable linker ensures that the label can, if required, be removed after detection, avoiding any interfering signal with any labelled nucleotide incorporated subsequently. The use of the term “cleavable linker” is not meant to imply that the whole linker is required to be removed from the nucleotide base. The cleavage site can be located at a position on the linker that ensures that part of the linker remains attached to the nucleotide base after cleavage. The linker can be attached at any position on the nucleotide base provided that Watson- Crick base pairing can still be carried out. In the context of purine bases, it is preferred if the linker is attached via the 7-position of the purine or the preferred deazapurine analogue, via an 8- modified purine, via an N-6 modified adenosine or an N-2 modified guanine. For pyrimidines, attachment is preferably via the 5-position on cytidine, thymidine or uracil and the N-4 position on cytosine.

[0037] The term “cleavable linker” or “cleavable moiety” as used herein refers to a divalent or monovalent, respectively, moiety which is capable of being separated (e.g., detached, split, disconnected, hydrolyzed, a stable bond within the moiety is broken) into distinct entities. A cleavable linker is cleavable (e.g., specifically cleavable) in response to external stimuli (e.g., enzymes, nucleophilic/basic reagents, reducing agents, photo-irradiation, electrophilic/acidic reagents, organometallic and metal reagents, or oxidizing reagents). A chemically cleavable linker refers to a linker which is capable of being split in response to the presence of a chemical (e.g., acid, base, oxidizing agent, reducing agent, Pd(0), tris-(2-carboxyethyl)phosphine, dilute nitrous acid, fluoride, tris(3-hydroxypropyl)phosphine), sodium dithionite (Na2S2O4), or hydrazine (N2H4)). A chemically cleavable linker is non-enzymatically cleavable. In embodiments, the cleavable linker is cleaved by contacting the cleavable linker with a cleaving agent. In embodiments, the cleaving agent is a phosphine containing reagent (e.g., TCEP or THPP), sodium dithionite (Na2S2O4), weak acid, hydrazine (N2H4), Pd(0), or light-irradiation (e.g., ultraviolet radiation). In embodiments, cleaving includes removing. A “cleavable site” or “scissile linkage” in the context of a polynucleotide is a site which allows controlled cleavage of the polynucleotide strand (e.g., the linker, the primer, or the polynucleotide) by chemical, enzymatic, or photochemical means known in the art and described herein. A scissile site may refer to the linkage of a nucleotide between two other nucleotides in a nucleotide strand (i.e., an internucleosidic linkage). In embodiments, the scissile linkage can be located at any position within the one or more nucleic acid molecules, including at or near a terminal end (e.g., the 3' end of an oligonucleotide) or in an interior portion of the one or more nucleic acid molecules. In embodiments, conditions suitable for separating a scissile linkage include a modulating the pH and/or the temperature. In embodiments, a scissile site can include at least one acid-labile linkage. For example, an acid-labile linkage may include a phosphoramidate linkage. In embodiments, a phosphoramidate linkage can be hydrolysable under acidic conditions, including mild acidic conditions such as trifluoroacetic acid and a suitable temperature (e.g., 30°C), or other conditions known in the art, for example Matthias Mag, et al Tetrahedron Letters, Volume 33, Issue 48, 1992, 7319-7322. In embodiments, the scissile site can include at least one photolabile internucleosidic linkage (e.g., o-nitrobenzyl linkages, as described in Walker et al, J. Am. Chem. Soc. 1988, 110, 21, 7170-7177), such as o-nitrobenzyloxymethyl or p-nitrobenzyloxymethyl group(s). In embodiments, the scissile site includes at least one uracil nucleobase. In embodiments, a uracil nucleobase can be cleaved with a uracil DNA glycosylase (UDG) or Formamidopyrimidine DNA Glycosylase Fpg. In embodiments, the scissile linkage site includes a sequence-specific nicking site having a nucleotide sequence that is recognized and nicked by a nicking endonuclease enzyme or a uracil DNA glycosylase. Cleavage agents used in methods described herein may be selected from nicking endonucleases, DNA glycosylases, or any singlestranded cleavage agents described in further detail elsewhere herein. Enzymes for cleavage of single- stranded DNA may be used for cleaving heteroduplexes in the vicinity of mismatched bases, D-loops, heteroduplexes formed between two strands of DNA which differ by a single base, an insertion or deletion. Mismatch recognition proteins that cleave one strand of the mismatched DNA in the vicinity of the mismatch site may be used as cleavage agents. Nonenzymatic cleaving may also be done through photodegredation of a linker introduced through a custom oligonucleotide used in a PCR reaction.

[0038] As used herein, the term “modified nucleotide” refers to nucleotide modified in some manner. Typically, a nucleotide contains a single 5-carbon sugar moiety, a single nitrogenous base moiety and 1 to three phosphate moieties. In embodiments, a nucleotide can include a blocking moiety and/or a label moiety. A blocking moiety on a nucleotide prevents formation of a covalent bond between the 3’ hydroxyl moiety of the nucleotide and the 5’ phosphate of another nucleotide. A blocking moiety on a nucleotide can be reversible, whereby the blocking moiety can be removed or modified to allow the 3’ hydroxyl to form a covalent bond with the 5’ phosphate of another nucleotide. A blocking moiety can be effectively irreversible under particular conditions used in a method set forth herein. In embodiments, the blocking moiety is attached to the 3’ oxygen of the nucleotide and is independently -NH2, -CN, -CH3, C2-C6 allyl e.g., -CH2- CH=CH2), methoxyalkyl (e.g., -CH2-O-CH3), or -C E ?. In embodiments, the blocking moiety is

attached to the 3’ oxygen of the nucleotide and is independently

. A label moiety of a modified nucleotide can be any moiety that allows the nucleotide to be detected, for example, using a spectroscopic method. Exemplary label moieties are fluorescent labels, mass labels, chemiluminescent labels, electrochemical labels, detectable labels and the like. One or more of the above moieties can be absent from a nucleotide used in the methods and compositions set forth herein. For example, a nucleotide can lack a label moiety or a blocking moiety or both. Examples of nucleotide analogues include, without limitation, 7-deaza-adenine, 7- deaza-guanine, the analogues of deoxynucleotides shown herein, analogues in which a label is attached through a cleavable linker to the 5-position of cytosine or thymine or to the 7-position of deaza-adenine or deaza-guanine, and analogues in which a small chemical moiety is used to cap the OH group at the 3 ’-position of deoxyribose. Nucleotide analogues and DNA polymerase- based DNA sequencing are also described in U.S. Patent No. 6,664,079, which is incorporated herein by reference in its entirety for all purposes. Non-limiting examples of detectable labels include labels including fluorescent dyes, biotin, digoxin, haptens, and epitopes. In general, a dye is a molecule, compound, or substance that can provide an optically detectable signal, such as a colorimetric, luminescent, bioluminescent, chemiluminescent, phosphorescent, or fluorescent signal. In embodiments, the dye is a fluorescent dye. Non-limiting examples of dyes, some of which are commercially available, include CF dyes (Biotium, Inc.), Alexa Fluor dyes (Thermo Fisher), DyLight dyes (Thermo Fisher), Cy dyes (GE Healthscience), IRDyes (Li-Cor Biosciences, Inc.), and HiLyte dyes (Anaspec, Inc.). In embodiments, the label is a fluorophore.

[0039] In some embodiments, a nucleic acid includes a label. As used herein, the term “label” or “labels” is used in accordance with their plain and ordinary meanings and refer to molecules that can directly or indirectly produce or result in a detectable signal either by themselves or upon interaction with another molecule. Non-limiting examples of detectable labels include fluorescent dyes, biotin, digoxin, haptens, and epitopes. In general, a dye is a molecule, compound, or substance that can provide an optically detectable signal, such as a colorimetric, luminescent, bioluminescent, chemiluminescent, phosphorescent, or fluorescent signal. In embodiments, the label is a dye. In embodiments, the dye is a fluorescent dye. Non-limiting examples of dyes, some of which are commercially available, include CF dyes (Biotium, Inc.), Alexa Fluor dyes (Thermo Fisher), DyLight dyes (Thermo Fisher), Cy dyes (GE Healthscience), IRDyes (Li-Cor Biosciences, Inc.), and HiLyte dyes (Anaspec, Inc.). In embodiments, a particular nucleotide type is associated with a particular label, such that identifying the label identifies the nucleotide with which it is associated. In embodiments, the label is luciferin that reacts with luciferase to produce a detectable signal in response to one or more bases being incorporated into an elongated complementary strand, such as in pyrosequencing. In embodiment, a nucleotide includes a label (such as a dye). In embodiments, the label is not associated with any particular nucleotide, but detection of the label identifies whether one or more nucleotides having a known identity were added during an extension step (such as in the case of pyrosequencing). Examples of detectable agents (i.e., labels) include imaging agents, including fluorescent and luminescent substances, molecules, or compositions, including, but not limited to, a variety of organic or inorganic small molecules commonly referred to as “dyes,” “labels,” or “indicators.” Examples include fluorescein, rhodamine, acridine dyes, Alexa dyes, and cyanine dyes. In embodiments, the detectable moiety is a fluorescent molecule (e.g, acridine dye, cyanine, dye, fluorine dye, oxazine dye, phenanthridine dye, or rhodamine dye). In embodiments, the detectable moiety is a fluorescent molecule (e.g, acridine dye, cyanine, dye, fluorine dye, oxazine dye, phenanthridine dye, or rhodamine dye). The term “cyanine” or “cyanine moiety” as described herein refers to a detectable moiety containing two nitrogen groups separated by a polymethine chain. In embodiments, the cyanine moiety has 3 methine structures (i.e., cyanine 3 or Cy3). In embodiments, the cyanine moiety has 5 methine structures (i.e., cyanine 5 or Cy5). In embodiments, the cyanine moiety has 7 methine structures (i.e., cyanine 7 or Cy7).

[0040] The term “nucleoside” refers, in the usual and customary sense, to a glycosylamine including a nucleobase and a five-carbon sugar (ribose or deoxyribose). Non-limiting examples of nucleosides include cytidine, uridine, adenosine, guanosine, thymidine and inosine. Nucleosides may be modified at the base and/or the sugar. The term “nucleotide” refers, in the usual and customary sense, to a single unit of a polynucleotide, i.e., a monomer. Nucleotides can be ribonucleotides, deoxyribonucleotides, or modified versions thereof. Examples of polynucleotides contemplated herein include single and double stranded DNA, single and double stranded RNA, and hybrid molecules having mixtures of single and double stranded DNA and RNA. Examples of nucleic acid, e.g., polynucleotides contemplated herein include any types of RNA, e.g., mRNA, siRNA, miRNA, and guide RNA and any types of DNA, genomic DNA, plasmid DNA, and minicircle DNA, and any fragments thereof. The term “duplex” in the context of polynucleotides refers, in the usual and customary sense, to double strandedness.

[0041] The terms “identical” or percent “identity,” in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same (i.e., about 60% identity, preferably 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher identity over a specified region, when compared and aligned for maximum correspondence over a comparison window or designated region) as measured using a BLAST or BLAST 2.0 sequence comparison algorithms with default parameters described below, or by manual alignment and visual inspection (see, e.g., NCBI web site www.ncbi.nlm.nih.gov/BLAST/ or the like). Such sequences are then said to be “substantially identical.” This definition also refers to, or may be applied to, the complement of a test sequence. The definition also includes sequences that have deletions and/or additions, as well as those that have substitutions. As described below, the preferred algorithms can account for gaps and the like. Preferably, identity exists over a region that is at least about 25 amino acids or nucleotides in length, or more preferably over a region that is 50-100 amino acids or nucleotides in length.

[0042] As used herein, the term “removable” group, e.g., a label or a blocking group or protecting group, is used in accordance with its plain and ordinary meaning and refers to a chemical group that can be removed from a nucleotide analogue such that a DNA polymerase can extend the nucleic acid (e.g., a primer or extension product) by the incorporation of at least one additional nucleotide. Removal may be by any suitable method, including enzymatic, chemical, or photolytic cleavage. Removal of a removable group, e.g., a blocking group, does not require that the entire removable group be removed, only that a sufficient portion of it be removed such that a DNA polymerase can extend a nucleic acid by incorporation of at least one additional nucleotide using a nucleotide or nucleotide analogue. In general, the conditions under which a removable group is removed are compatible with a process employing the removable group (e.g., an amplification process or sequencing process).

[0043] As used herein, the terms “reversible blocking groups” and “reversible terminators” are used in accordance with their plain and ordinary meanings and refer to a blocking moiety located, for example, at the 3’ position of a modified nucleotide and may be a chemically cleavable moiety such as an allyl group, an azidomethyl group or a methoxymethyl group, or may be an enzymatically cleavable group such as a phosphate ester. Non-limiting examples of nucleotide blocking moi eties are described in applications WO 2004/018497, WO 96/07669, U.S. Pat. Nos. 7,057,026, 7,541,444, 5,763,594, 5,808,045, 5,872,244 and 6,232,465 the contents of which are incorporated herein by reference in their entirety. The nucleotides may be labelled or unlabeled. They may be modified with reversible terminators useful in methods provided herein and may be 3’-O-blocked reversible or 3’-unblocked reversible terminators. In nucleotides with 3’-O-blocked reversible terminators, the blocking group -OR [reversible terminating (capping) group] is linked to the oxygen atom of the 3 ’-OH of the pentose, while the label is linked to the base, which acts as a reporter and can be cleaved. The 3’-O-blocked reversible terminators are known in the art, and may be, for instance, a 3’-ONH2 reversible terminator, a 3’-O-allyl reversible terminator, or a 3’- O-azidomethyl reversible terminator. In embodiments, the reversible terminator moiety is attached to the 3 ’-oxygen of the nucleotide, having the formula:

,

wherein the 3’ oxygen of the nucleotide is not shown in the formulae above. The term “allyl” as described herein refers to an unsubstituted methylene attached to a vinyl group (i.e., -CH=CH2).

In embodiments, the reversible terminator moiety is

as described in U.S. Patent 10,738,072, which is incorporated herein by reference for all purposes. For example, a nucleotide including a reversible terminator moiety may be represented by the formula:

O O O

HO—

Nucleobase-Cleavable linker — Label H AH AH

''Reversible Terminator moiety y < .< < < , where the nucleobase is adenine or adenine analogue, thymine or thymine analogue, guanine or guanine analogue, or cytosine or cytosine analogue.

[0044] In some embodiments, a nucleic acid (e.g., a probe or a primer) includes a molecular identifier or a molecular barcode. As used herein, the term “molecular barcode” (which may be referred to as a “tag”, a “barcode”, a “molecular identifier”, an “identifier sequence” or a “unique molecular identifier” (UMI)) refers to any material (e.g., a nucleotide sequence, a nucleic acid molecule feature) that is capable of distinguishing an individual molecule in a large heterogeneous population of molecules. In embodiments, a barcode is unique in a pool of barcodes that differ from one another in sequence, or is uniquely associated with a particular sample polynucleotide in a pool of sample polynucleotides. In embodiments, every barcode in a pool of adapters is unique, such that sequencing reads including the barcode can be identified as originating from a single sample polynucleotide molecule on the basis of the barcode alone. In other embodiments, individual barcode sequences may be used more than once, but adapters including the duplicate barcodes are associated with different sequences and/or in different combinations of barcoded adaptors, such that sequence reads may still be uniquely distinguished as originating from a single sample polynucleotide molecule on the basis of a barcode and adjacent sequence information (e.g., sample polynucleotide sequence, and/or one or more adjacent barcodes). In embodiments, barcodes are about or at least about 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 40, 50, 75 or more nucleotides in length. In embodiments, barcodes are shorter than 20, 15, 10, 9, 8, 7, 6, or 5 nucleotides in length. In embodiments, barcodes are about 10 to about 50 nucleotides in length, such as about 15 to about 40 or about 20 to about 30 nucleotides in length. In a pool of different barcodes, barcodes may have the same or different lengths. In general, barcodes are of sufficient length and include sequences that are sufficiently different to allow the identification of sequencing reads that originate from the same sample polynucleotide molecule. In embodiments, each barcode in a plurality of barcodes differs from every other barcode in the plurality by at least three nucleotide positions, such as at least 3, 4, 5, 6, 7, 8, 9, 10, or more nucleotide positions. In some embodiments, substantially degenerate barcodes may be known as random. In some embodiments, a barcode may include a nucleic acid sequence from within a pool of known sequences. In some embodiments, the barcodes may be pre-defined. In embodiments, the barcodes are selected to form a known set of barcodes, e.g., the set of barcodes may be distinguished by a particular Hamming distance. In embodiments, each barcode sequence is unique within the known set of barcodes. In embodiments, each barcode sequence is associated with a particular oligonucleotide probe.

[0045] In embodiments, a nucleic acid (e.g., an adapter or primer) includes a sample barcode. In general, a “sample barcode” is a nucleotide sequence that is sufficiently different from other sample barcode to allow the identification of the sample source based on sample barcode sequence(s) with which they are associated. In embodiments, a plurality of nucleotides (e.g., all nucleotides from a particular sample source, or sub-sample thereof) are joined to a first sample barcode, while a different plurality of nucleotides (e.g., all nucleotides from a different sample source, or different subsample) are joined to a second sample barcode, thereby associating each plurality of polynucleotides with a different sample barcode indicative of sample source. In embodiments, each sample barcode in a plurality of sample barcodes differs from every other sample barcode in the plurality by at least three nucleotide positions, such as at least 3, 4, 5, 6, 7, 8, 9, 10, or more nucleotide positions. In some embodiments, substantially degenerate sample barcodes may be known as random. In some embodiments, a sample barcode may include a nucleic acid sequence from within a pool of known sequences. In some embodiments, the sample barcodes may be pre-defined. In embodiments, the sample barcode includes about 1 to about 10 nucleotides. In embodiments, the sample barcode includes about 3, 4, 5, 6, 7, 8, 9, or about 10 nucleotides. In embodiments, the sample barcode includes about 3 nucleotides. In embodiments, the sample barcode includes about 5 nucleotides. In embodiments, the sample barcode includes about 7 nucleotides. In embodiments, the sample barcode includes about 10 nucleotides. In embodiments, the sample barcode includes about 6 to about 10 nucleotides.

[0046] As used herein, the term “DNA polymerase” and “nucleic acid polymerase” are used in accordance with their plain ordinary meanings and refer to enzymes capable of synthesizing nucleic acid molecules from nucleotides (e.g., deoxyribonucleotides). Exemplary types of polymerases that may be used in the compositions and methods of the present disclosure include the nucleic acid polymerases such as DNA polymerase, DNA- or RNA-dependent RNA polymerase, and reverse transcriptase. In some cases, the DNA polymerase is 9°N polymerase or a variant thereof, E. Coli DNA polymerase I, Bacteriophage T4 DNA polymerase, Sequenase, Taq DNA polymerase, DNA polymerase from Bacillus stearothermophilus, Bst 2.0 DNA polymerase, 9°N polymerase (exo-)A485L/Y409V, Phi29 DNA Polymerase (cp29 DNA Polymerase), T7 DNA polymerase, DNA polymerase II, DNA polymerase III holoenzyme, DNA polymerase IV, DNA polymerase V, VentR DNA polymerase, Therminator™ II DNA Polymerase, Therminator™ III DNA Polymerase, or or Therminator™ IX DNA Polymerase. In embodiments, the polymerase is a protein polymerase. Typically, a DNA polymerase adds nucleotides to the 3’ - end of a DNA strand, one nucleotide at a time. In embodiments, the DNA polymerase is a Pol I DNA polymerase, Pol II DNA polymerase, Pol III DNA polymerase, Pol IV DNA polymerase, Pol V DNA polymerase, Pol P DNA polymerase, Pol p DNA polymerase, Pol DNA polymerase, Pol c DNA polymerase, Pol a DNA polymerase, Pol 5 DNA polymerase, Pol a DNA polymerase, Pol r] DNA polymerase, Pol r DNA polymerase, Pol K DNA polymerase, Pol C, DNA polymerase, Pol y DNA polymerase, Pol 9 DNA polymerase, Pol u DNA polymerase, or a thermophilic nucleic acid polymerase (e.g. Therminator y, 9°N polymerase (exo-), Therminator II, Therminator III, or Therminator IX). In embodiments, the DNA polymerase is a modified archaeal DNA polymerase. In embodiments, the polymerase is a reverse transcriptase. In embodiments, the polymerase is a mutant P. abyssi polymerase (e.g., such as a mutant P. abyssi polymerase described in WO 2018/148723 or WO 2020/056044). In embodiments, the polymerase is an enzyme described in US 2021/0139884. For example, a polymerase catalyzes the addition of a next correct nucleotide to the 3'-OH group of the primer via a phosphodiester bond, thereby chemically incorporating the nucleotide into the primer. Optionally, the polymerase used in the provided methods is a processive polymerase. Optionally, the polymerase used in the provided methods is a distributive polymerase.

[0047] As used herein, the term “thermophilic nucleic acid polymerase” refers to a family of DNA polymerases (e.g., 9°N™) and mutants thereof derived from the DNA polymerase originally isolated from the hyperthermophilic archaea, Thermococcus sp. 9 degrees N-7, found in hydrothermal vents at that latitude (East Pacific Rise) (Southworth MW, et al. PNAS.

1996;93( 11): 5281 -5285). A thermophilic nucleic acid polymerase is a member of the family B DNA polymerases. Site-directed mutagenesis of the 3’-5’ exo motif I (Asp-Ile-Glu or DIE) to AIA, AIE, EIE, EID or DIA yielded polymerase with no detectable 3’ exonuclease activity. Mutation to Asp-Ile-Asp (DID) resulted in reduction of 3’-5’ exonuclease specific activity to <1% of wild type, while maintaining other properties of the polymerase including its high strand displacement activity. The sequence AIA (D141 A, E143A) was chosen for reducing exonuclease. Subsequent mutagenesis of key amino acids results in an increased ability of the enzyme to incorporate dideoxynucleotides, ribonucleotides and acyclonucleotides (e.g., Therminator II enzyme from New England Biolabs with D141 A / E143A / Y409V / A485L mutations); 3’- amino-dNTPs, 3’-azido-dNTPs and other 3 ’-modified nucleotides (e.g., NEB Therminator III DNA Polymerase with D141 A / E143A / L408S / Y409A / P410V mutations, NEB Therminator IX DNA polymerase), or y-phosphate labeled nucleotides (e.g., Therminator y: D141 A / E143A / W355A / L408W / R460A / Q461S / K464E / D480V / R484W / A485L). Typically, these enzymes do not have 5 ’-3’ exonuclease activity. Additional information about thermophilic nucleic acid polymerases may be found in (Southworth MW, et al. PNAS. 1996;93(11): 5281 - 5285; Bergen K, et al. ChemBioChem. 2013; 14(9): 1058-1062; Kumar S, et al. Scientific Reports. 2012;2:684; Fuller CW, et al. 2016; 113(19): 5233-5238; Guo J, et al. Proceedings of the National Academy of Sciences of the United States of America. 2008;105(27):9145-9150), which are incorporated herein in their entirety for all purposes.

[0048] As used herein, the term “strand-displacing polymerase” refers to a type of polymerase (e.g., a DNA polymerase or reverse transcriptase) that is able to synthesize new DNA strands while simultaneously displacing the template strand in a single reaction. Strand-displacing polymerases are able to displace one or more nucleotides, for example 10 or 100 or more nucleotides, that are downstream from the enzyme. Strand-displacing polymerases are commonly used in isothermal amplification techniques, such as loop-mediated isothermal amplification (LAMP) and multiple displacement amplification (MDA). One example of a strand-displacing polymerase is the Bst DNA polymerase, which is commonly used in LAMP reactions. Another example is the phi29 DNA polymerase, which is often used in RCA reactions.

[0049] As used herein, the term “exonuclease activity” is used in accordance with its ordinary meaning in the art, and refers to the removal of a nucleotide from a nucleic acid by an enzyme (e.g. DNA polymerase, a lambda exonuclease, Exo I, Exo III, T5, Exo V, Exo VII or the like). For example, during polymerization, nucleotides are added to the 3’ end of the primer strand. Occasionally a DNA polymerase incorporates an incorrect nucleotide to the 3'-OH terminus of the primer strand, wherein the incorrect nucleotide cannot form a hydrogen bond to the corresponding base in the template strand. Such a nucleotide, added in error, is removed from the primer as a result of the 3' to 5' exonuclease activity of the DNA polymerase. In embodiments, exonuclease activity may be referred to as “proofreading.” When referring to 3’-5’ exonuclease activity, it is understood that the DNA polymerase facilitates a hydrolyzing reaction that breaks phosphodiester bonds at the 3’ end of a polynucleotide chain to excise the nucleotide. In embodiments, 3 ’-5’ exonuclease activity refers to the successive removal of nucleotides in single-stranded DNA in a 3’ — 5’ direction, releasing deoxyribonucleoside 5 ’-monophosphates one after another. Methods for quantifying exonuclease activity are known in the art, see for example Southworth et al, PNAS Vol 93, 8281-8285 (1996). In embodiments, 5’-3’ exonuclease activity refers to the successive removal of nucleotides in double-stranded DNA in a 5’ — 3’ direction. In embodiments, the 5 ’-3’ exonuclease is lambda exonuclease. For example, lambda exonuclease catalyzes the removal of 5’ mononucleotides from duplex DNA, with a preference for 5’ phosphorylated double-stranded DNA. In other embodiments, the 5 ’-3’ exonuclease is E. coli DNA Polymerase I.

[0050] As used herein, the term “endonuclease” refers to enzymes that cleave the phosphodiester bond within a polynucleotide chain. The polynucleotide may be double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), RNA, double-stranded hybrids of DNA and RNA, and synthetic DNA (for example, containing bases other than A, C, G, and T). An endonuclease may cut a polynucleotide symmetrically, leaving “blunt” ends, or in positions that are not directly opposing, creating overhangs, which may be referred to as “sticky ends.” An endonuclease may cut a double-stranded polynucleotide on a single strand. The methods and compositions described herein may be applied to cleavage sites generated by endonucleases. In some alternatives of the system, the system can further provide nucleic acids that encode an endonuclease, such as Cas9, TALEN, or MegaTAL, or a fusion protein including a domain of an endonuclease, for example, Cas9, TALEN, or MegaTAL, or one or more portion thereof. These examples are not meant to be limiting and other endonucleases and alternatives of the system and methods including other endonucleases and variants and modifications of these exemplary alternatives are possible without undue experimentation. All such variations and modifications are within the scope of the current teachings.

[0051] As used herein, the term “nicking endonuclease” refers to any enzyme, naturally occurring or engineered, that is capable of breaking a phosphodiester bond on a single DNA strand, leaving a 3 '-hydroxyl at a defined sequence. Nicking endonucleases can be engineered by modifying restriction enzymes to eliminate cutting activity for one DNA strand, or produced by fusing a nicking subunit to a DNA binding domain, for example, zinc fingers and DNA recognition domains from transcription activator-like effectors.

[0052] As used herein, “nick” generally refers to enzymatic cleavage of only one strand of a double-stranded nucleic acid at a particular region, while leaving the other strand intact, regardless of whether one or more bases are removed. In some cases, one or more bases are removed while in other cases no bases are removed and only phosphodiester bonds are broken. In some instances, such cleavage events leave behind intact double-stranded regions lacking nicks that are a short distance apart from each other on the double-stranded nucleic acid, for example a distance of about or at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 bases or more. In some cases, the distance between the intact double-stranded regions is equal to or less than 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, or 2 bases. In some instances, the distance between the intact double-stranded regions is 2 to 10 bases, 3 to 9 bases, or 4 to 8 bases.

[0053] As used herein, the term “incorporating” or “chemically incorporating,” when used in reference to a primer and cognate nucleotide, refers to the process of joining the cognate nucleotide to the primer or extension product thereof by formation of a phosphodiester bond.

[0054] As used herein, the term “selective” or “selectivity” or the like of a compound refers to the compound’s ability to discriminate between molecular targets. For example, a chemical reagent may selectively modify one nucleotide type in that it reacts with one nucleotide type (e.g., cytosines) and not other nucleotide types (e.g., adenine, thymine, or guanine). When used in the context of sequencing, such as in “selectively sequencing,” this term refers to sequencing one or more target polynucleotides from an original starting population of polynucleotides, and not sequencing non-target polynucleotides from the starting population. Typically, selectively sequencing one or more target polynucleotides involves differentially manipulating the target polynucleotides based on known sequence. For example, target polynucleotides may be hybridized to a probe oligonucleotide that may be labeled (such as with a member of a binding pair) or bound to a surface. In embodiments, hybridizing a target polynucleotide to a probe oligonucleotide includes the step of displacing one strand of a double-stranded nucleic acid. Probe-hybridized target polynucleotides may then be separated from non-hybridized polynucleotides, such as by removing probe-bound polynucleotides from the starting population or by washing away polynucleotides that are not bound to a probe. The result is a selected subset of the starting population of polynucleotides, which is then subjected to sequencing, thereby selectively sequencing the one or more target polynucleotides.

[0055] As used herein, the term “template polynucleotide” refers to any polynucleotide molecule that may be bound by a polymerase and utilized as a template for nucleic acid synthesis. A template polynucleotide may be a target polynucleotide. In general, the term “target polynucleotide” refers to a nucleic acid molecule or polynucleotide in a starting population of nucleic acid molecules having a target sequence whose presence, amount, and/or nucleotide sequence, or changes in one or more of these, are desired to be determined. The target sequence may be a portion of a gene, a regulatory sequence, genomic DNA, cDNA, RNA including mRNA, miRNA, rRNA, or others. The target sequence may be a target sequence from a sample or a secondary target such as a product of an amplification reaction. A target polynucleotide is not necessarily any single molecule or sequence. For example, a target polynucleotide may be any one of a plurality of target polynucleotides in a reaction, or all polynucleotides in a given reaction, depending on the reaction conditions. For example, in a nucleic acid amplification reaction with random primers, all polynucleotides in a reaction may be amplified. As a further example, a collection of targets may be simultaneously assayed using polynucleotide primers directed to a plurality of targets in a single reaction. As yet another example, all or a subset of polynucleotides in a sample may be modified by the addition of a primer-binding sequence (such as by the ligation of adapters containing the primer binding sequence), rendering each modified polynucleotide a target polynucleotide in a reaction with the corresponding primer polynucleotide(s). In embodiments, the template polynucleotide includes a target nucleic acid sequence and one or more barcode sequences. In embodiments, the template polynucleotide is a barcode sequence. A “target sequence”, as used herein, refers to a sequence of a splint oligonucleotide that is the same, or substantially the same, as a sequence in a target polynucleotide (i.e., the target sequence of the splint oligonucleotide is the same, or substantially the same, as the target sequence in the target polynucleotide). In embodiments, the target sequence is a known sequence. In embodiments, the target sequence is selected from a set of known target sequences. In embodiments, the target sequence is located 5’ of the probe hybridization sequence of the target polynucleotide. A “subject sequence”, as used herein, refers to the sequence of interest in a target polynucleotide. For example, an oligonucleotide probe may be hybridized upstream of a subject sequence of a target polynucleotide and extending the oligonucleotide probe incorporates a sequence complementary to the subject sequence (i.e., a subject sequence complement) into the oligonucleotide probe. The extended oligonucleotide probe may then be processed further (e.g., circularized and/or amplified), and the subject sequence detected by, e.g., sequencing.

[0056] In embodiments, a target polynucleotide is a cell-free polynucleotide. In general, the terms “cell-free,” “circulating,” and “extracellular” as applied to polynucleotides (e.g. “cell-free DNA” (cfDNA) and “cell-free RNA” (cfRNA)) are used interchangeably to refer to polynucleotides present in a sample from a subject or portion thereof that can be isolated or otherwise manipulated without applying a lysis step to the sample as originally collected (e.g., as in extraction from cells or viruses). Cell-free polynucleotides are thus unencapsulated or “free” from the cells or viruses from which they originate, even before a sample of the subject is collected. Cell-free polynucleotides may be produced as a byproduct of cell death (e.g., apoptosis or necrosis) or cell shedding, releasing polynucleotides into surrounding body fluids or into circulation. Accordingly, cell-free polynucleotides may be isolated from a non-cellular fraction of blood (e.g., serum or plasma), from other bodily fluids (e.g., urine), or from non-cellular fractions of other types of samples.

[0057] As used herein, the terms “specific”, “specifically”, “specificity”, or the like of a compound refers to the compound’s ability to cause a particular action, such as binding, to a particular molecular target with minimal or no action to other proteins in the cell.

[0058] The terms “attached,” “bind,” and “bound” as used herein are used in accordance with their plain and ordinary meanings and refer to an association between atoms or molecules. The association can be direct or indirect. For example, attached molecules may be directly bound to one another, e.g., by a covalent bond or non-covalent bond (e.g. electrostatic interactions (e.g. ionic bond, hydrogen bond, halogen bond), van der Waals interactions (e.g. dipole-dipole, dipole- induced dipole, London dispersion), ring stacking (pi effects), hydrophobic interactions and the like). As a further example, two molecules may be bound indirectly to one another by way of direct binding to one or more intermediate molecules, thereby forming a complex.

[0059] “Specific binding” is where the binding is selective between two molecules. A particular example of specific binding is that which occurs between an antibody and an antigen. Typically, specific binding can be distinguished from non-specific when the dissociation constant (KD) is less than about 1 x 10-5 M or less than about 1 x 10-6 M or 1 x 10-7 M. Specific binding can be detected, for example, by ELISA, immunoprecipitation, coprecipitation, with or without chemical crosslinking, two-hybrid assays and the like. In embodiments, the KD (equilibrium dissociation constant) between two specific binding molecules is less than 10-6 M, less than 10-7 M, less than 10-8 M, less than 10-9 M, less than 10-9 M, less than 10-11 M, or less than about 10-12 M or less.

[0060] As used herein, the terms “sequencing”, “sequence determination”, “determining a nucleotide sequence”, and the like include determination of a partial or complete sequence information (e.g., a sequence) of a polynucleotide being sequenced, and particularly physical processes for generating such sequence information. That is, the term includes sequence comparisons, consensus sequence determination, contig assembly, fingerprinting, and like levels of information about a target polynucleotide, as well as the express identification and ordering of nucleotides in a target polynucleotide. The term also includes the determination of the identification, ordering, and locations of one, two, or three of the four types of nucleotides within a target polynucleotide. In some embodiments, a sequencing process described herein includes contacting a template and an annealed primer with a suitable polymerase under conditions suitable for polymerase extension and/or sequencing.

[0061] As used herein, the term “polymer” refers to macromolecules having one or more structurally unique repeating units. The repeating units are referred to as “monomers,” which are polymerized for the polymer. Typically, a polymer is formed by monomers linked in a chain-like structure. A polymer formed entirely from a single type of monomer is referred to as a “homopolymer.” A polymer formed from two or more unique repeating structural units may be referred to as a “copolymer.” A polymer may be linear or branched, and may be random, block, polymer brush, hyperbranched polymer, bottlebrush polymer, dendritic polymer, or polymer micelles. The term “polymer” includes homopolymers, copolymers, tripolymers, tetra polymers and other polymeric molecules made from monomeric subunits. Copolymers include alternating copolymers, periodic copolymers, statistical copolymers, random copolymers, block copolymers, linear copolymers and branched copolymers. The term “polymerizable monomer” is used in accordance with its meaning in the art of polymer chemistry and refers to a compound that may covalently bind chemically to other monomer molecules (such as other polymerizable monomers that are the same or different) to form a polymer.

[0062] Polymers can be hydrophilic, hydrophobic or amphiphilic, as known in the art. Thus, “hydrophilic polymers” are substantially miscible with water and include, but are not limited to, polyethylene glycol and the like. “Hydrophobic polymers” are substantially immiscible with water and include, but are not limited to, polyethylene, polypropylene, polybutadiene, polystyrene, polymers disclosed herein, and the like. “Amphiphilic polymers” have both hydrophilic and hydrophobic properties and are typically copolymers having hydrophilic segment(s) and hydrophobic segment(s). Polymers include homopolymers, random copolymers, and block copolymers, as known in the art. The term “homopolymer” refers, in the usual and customary sense, to a polymer having a single monomeric unit. The term “copolymer” refers to a polymer derived from two or more monomeric species. The term “random copolymer” refers to a polymer derived from two or more monomeric species with no preferred ordering of the monomeric species. The term “block copolymer” refers to polymers having two or homopolymer subunits linked by covalent bond. Thus, the term “hydrophobic homopolymer” refers to a homopolymer which is hydrophobic. The term “hydrophobic block copolymer” refers to two or more homopolymer subunits linked by covalent bonds and which is hydrophobic.

[0063] As used herein, the term “hydrogel” refers to a three-dimensional polymeric structure that is substantially insoluble in water, but which is capable of absorbing and retaining large quantities of water to form a substantially stable, often soft and pliable, structure. In embodiments, water can penetrate in between polymer chains of a polymer network, subsequently causing swelling and the formation of a hydrogel. In embodiments, hydrogels are super-absorbent (e.g., containing more than about 90% water) and can be comprised of natural or synthetic polymers.

[0064] As used herein, the term “substrate” refers to a solid support material. The substrate can be non-porous or porous. The substrate can be rigid or flexible. As used herein, the terms “solid support” and “solid surface” refers to discrete solid or semi-solid surface. A solid support may encompass any type of solid, porous, or hollow sphere, ball, cylinder, or other similar configuration composed of plastic, ceramic, metal, or polymeric material (e.g., hydrogel) onto which a nucleic acid may be immobilized (e.g., covalently or non-covalently). A nonporous substrate generally provides a seal against bulk flow of liquids or gases. Exemplary solid supports include, but are not limited to, glass and modified or functionalized glass, plastics (including acrylics, polystyrene and copolymers of styrene and other materials, polypropylene, polyethylene, polybutylene, polyurethanes, Teflon™, cyclic olefin copolymers, polyimides etc.), nylon, ceramics, resins, Zeonor, silica or silica-based materials including silicon and modified silicon, carbon, metals, inorganic glasses, optical fiber bundles, photopattemable dry film resists, UV-cured adhesives and polymers. Particularly useful solid supports for some embodiments have at least one surface located within a flow cell. Solid surfaces can also be varied in their shape depending on the application in a method described herein. For example, a solid surface useful herein can be planar, or contain regions which are concave or convex. In embodiments, the geometry of the concave or convex regions (e.g., wells) of the solid surface conform to the size and shape of the particle to maximize the contact between as substantially circular particle. In embodiments, the wells of an array are randomly located such that nearest neighbor features have random spacing between each other. Alternatively, in embodiments the spacing between the wells can be ordered, for example, forming a regular pattern. The term solid substrate is encompassing of a substrate (e.g., a flow cell) having a surface including a polymer coating covalently attached thereto. In embodiments, the solid substrate is a flow cell. The term “flow cell” as used herein refers to a chamber including a solid surface across which one or more fluid reagents can be flowed. Examples of flow cells and related fluidic systems and detection platforms that can be readily used in the methods of the present disclosure are described, for example, in Bentley et al., Nature 456:53-59 (2008). In certain embodiments a substrate includes a surface (e.g., a surface of a flow cell, a surface of a tube, a surface of a chip), for example a metal surface (e.g., steel, gold, silver, aluminum, silicon and copper). In embodiments a substrate (e.g., a substrate surface) is coated and/or includes functional groups and/or inert materials. In certain embodiments a substrate includes a bead, a chip, a capillary, a plate, a membrane, a wafer (e.g., silicon wafers), a comb, or a pin for example. In some embodiments a substrate includes a bead and/or a nanoparticle. A substrate can be made of a suitable material, non-limiting examples of which include a plastic or a suitable polymer (e.g., polycarbonate, poly(vinyl alcohol), poly(divinylbenzene), polystyrene, polyamide, polyester, polyvinylidene difluoride (PVDF), polyethylene, polyurethane, polypropylene, and the like), borosilicate, glass, nylon, Wang resin, Merrifield resin, metal (e.g., iron, a metal alloy, sepharose, agarose, polyacrylamide, dextran, cellulose and the like or combinations thereof. In embodiments a substrate includes a magnetic material (e.g., iron, nickel, cobalt, platinum, aluminum, and the like). In embodiments a substrate includes a magnetic bead (e.g., DYNABEADS®, hematite, AMPure XP). Magnets can be used to purify and/or capture nucleic acids bound to certain substrates (e.g., substrates including a metal or magnetic material). The flow cell is typically a glass slide containing small fluidic channels (e.g., a glass slide 75mm x 25mm x 1 mm having one or more channels), through which sequencing solutions (e.g., polymerases, nucleotides, and buffers) may traverse. Though typically glass, suitable flow cell materials may include polymeric materials, plastics, silicon, quartz (fused silica), Borofloat® glass, silica, silica-based materials, carbon, metals, an optical fiber or optical fiber bundles, sapphire, or plastic materials such as COCs and epoxies. The particular material can be selected based on properties desired for a particular use. For example, materials that are transparent to a desired wavelength of radiation are useful for analytical techniques that will utilize radiation of the desired wavelength. Conversely, it may be desirable to select a material that does not pass radiation of a certain wavelength (e.g., being opaque, absorptive, or reflective). In embodiments, the material of the flow cell is selected due to the ability to conduct thermal energy. In embodiments, a flow cell includes inlet and outlet ports and a flow channel extending there between.

[0065] The term “surface” is intended to mean an external part or external layer of a substrate. The surface can be in contact with another material such as a gas, liquid, gel, polymer, organic polymer, second surface of a similar or different material, metal, or coat. The surface, or regions thereof, can be substantially flat. The substrate and/or the surface can have surface features such as wells, pits, channels, ridges, raised regions, pegs, posts or the like.

[0066] The term “microplate”, or “multiwell container” as used herein, refers to a substrate including a surface, the surface including a plurality of reaction chambers separated from each other by interstitial regions on the surface. In embodiments, the microplate has dimensions as provided and described by American National Standards Institute (ANSI) and Society for Laboratory Automation And Screening (SLAS); for example the tolerances and dimensions set forth in ANSI SLAS 1-2004 (R2012); ANSI SLAS 2-2004 (R2012); ANSI SLAS 3-2004 (R2012); ANSI SLAS 4-2004 (R2012); and ANSI SLAS 6-2012, which are incorporated herein by reference. The dimensions of the microplate as described herein and the arrangement of the reaction chambers may be compatible with an established format for automated laboratory equipment. In embodiments, the device described herein provides methods for high-throughput screening. High-throughput screening (HTS) refers to a process that uses a combination of modern robotics, data processing and control software, liquid handling devices, and/or sensitive detectors, to efficiently process a large amount of (e.g., thousands, hundreds of thousands, or millions) samples in biochemical, genetic, or pharmacological experiments, either in parallel or in sequence, within a reasonably short period of time (e.g., days). Preferably, the process is amenable to automation, such as robotic simultaneous handling of 96 samples, 384 samples, 1536 samples or more. A typical HTS robot tests up to 100,000 to a few hundred thousand compounds per day. The samples are often in small volumes, such as no more than 1 mL, 500 pl, 200 pl, 100 pl, 50 pl or less. Through this process, one can rapidly identify active compounds, small molecules, antibodies, proteins or polynucleotides in a cell.

[0067] The reaction chambers may be provided as wells of a multiwell container (alternatively referred to as reaction chambers), for example a microplate may contain 2, 4, 6, 12, 24, 48, 96, 384, or 1536 sample wells. In embodiments, the 96 and 384 wells are arranged in a 2:3 rectangular matrix. In embodiments, the 24 wells are arranged in a 3:8 rectangular matrix. In embodiments, the 48 wells are arranged in a 3:4 rectangular matrix. In embodiments, the reaction chamber is a microscope slide (e.g., a glass slide about 75 mm by about 25 mm). In embodiments the slide is a concavity slide (e.g., the slide includes a depression). In embodiments, the slide includes a coating for enhanced cell adhesion (e.g., poly-L-lysine, silanes, carbon nanotubes, polymers, epoxy resins, or gold). In embodiments, the microplate is about 5 inches by about 3.33 inches, and includes a plurality of 5 mm diameter wells. In embodiments, the microplate is about 5 inches by about 3.33 inches, and includes a plurality of 6 mm diameter wells. In embodiments, the microplate is about 5 inches by about 3.33 inches, and includes a plurality of 7 mm diameter wells. In embodiments, the microplate is about 5 inches by about 3.33 inches, and includes a plurality of 7.5 mm diameter wells. In embodiments, the microplate is 5 inches by 3.33 inches, and includes a plurality of 7.5 mm diameter wells. In embodiments, the microplate is about 5 inches by about 3.33 inches, and includes a plurality of 8 mm diameter wells. In embodiments, the microplate is a flat glass or plastic tray in which an array of wells are formed, wherein each well can hold between from a few microliters to hundreds of microliters of fluid reagents and samples. In embodiments, the microplate has a rectangular shape that measures 127.7 mm±0.5 mm in length by 85.4 mm±0.5 mm in width, and includes 6, 12, 24, 48, or 96 wells, wherein each well has an average diameter of about 5-7 mm. In embodiments, the microplate has a rectangular shape that measures 127.7 mm±0.5 mm in length by 85.4 mm±0.5 mm in width, and includes 6, 12, 24, 48, or 96 wells, wherein each well has an average diameter of about 6 mm.

[0068] The term “well” refers to a discrete concave feature in a substrate having a surface opening that is completely surrounded by interstitial region(s) of the surface. Wells can have any of a variety of shapes at their opening in a surface including but not limited to round, elliptical, square, polygonal, or star shaped (i.e., star shaped with any number of vertices). The cross section of a well taken orthogonally with the surface may be curved, square, polygonal, hyperbolic, conical, or angular. The wells of a microplate are available in different shapes, for example F- Bottom: flat bottom; C-Bottom: bottom with minimal rounded edges; V-Bottom: V-shaped bottom; or U-Bottom: U-shaped bottom. In embodiments, the well is substantially square. In embodiments, the well is square. In embodiments, the well is F-bottom. In embodiments, the microplate includes 24 substantially round flat bottom wells. In embodiments, the microplate includes 48 substantially round flat bottom wells. In embodiments, the microplate includes 96 substantially round flat bottom wells. In embodiments, the microplate includes 384 substantially square flat bottom wells.

[0069] The discrete regions (i.e., features, wells) of the microplate may have defined locations in a regular array, which may correspond to a rectilinear pattern, circular pattern, hexagonal pattern, or the like. In embodiments, the pattern of wells includes concentric circles of regions, spiral patterns, rectilinear patterns, hexagonal patterns, and the like. In embodiments, the pattern of wells is arranged in a rectilinear or hexagonal pattern A regular array of such regions is advantageous for detection and data analysis of signals collected from the arrays during an analysis. These discrete regions are separated by interstitial regions. As used herein, the term “interstitial region” refers to an area in a substrate or on a surface that separates other areas of the substrate or surface. For example, an interstitial region can separate one concave feature of an array from another concave feature of the array. The two regions that are separated from each other can be discrete, lacking contact with each other. In another example, an interstitial region can separate a first portion of a feature from a second portion of a feature. In embodiments the interstitial region is continuous whereas the features are discrete, for example, as is the case for an array of wells in an otherwise continuous surface. The separation provided by an interstitial region can be partial or full separation. In embodiments, interstitial regions have a surface material that differs from the surface material of the wells (e.g., the interstitial region contains a photoresist and the surface of the well is glass). In embodiments, interstitial regions have a surface material that is the same as the surface material of the wells (e.g., both the surface of the interstitial region and the surface of well contain a polymer or copolymer).

[0070] As used herein, the term “sequencing reaction mixture” is used in accordance with its plain and ordinary meaning and refers to an aqueous mixture that contains the reagents necessary to allow dNTP or dNTP analogue (e.g., a modified nucleotide) to add a nucleotide to a DNA strand by a DNA polymerase. In embodiments, the sequencing reaction mixture includes a buffer. In embodiments, the buffer includes an acetate buffer, 3-(N-morpholino)propanesulfonic acid (MOPS) buffer, N-(2-Acetamido)-2-aminoethanesulfonic acid (ACES) buffer, phosphate-buffered saline (PBS) buffer, 4-(2 -hydroxy ethyl)- 1 -piperazineethanesulfonic acid (HEPES) buffer, N-(l,l- Dimethyl-2-hydroxyethyl)-3-amino-2-hydroxypropanesulfonic acid (AMPSO) buffer, borate buffer (e.g., borate buffered saline, sodium borate buffer, boric acid buffer), 2-Amino-2-methyl- 1,3-propanediol (AMPD) buffer, N-cyclohexyl-2-hydroxyl-3-aminopropanesulfonic acid (CAPSO) buffer, 2-Amino-2-methyl-l -propanol (AMP) buffer, 4-(cyclohexylamino)-l- butanesulfonic acid (CABS) buffer, glycine-NaOH buffer, N-Cyclohexyl-2-aminoethanesulfonic acid (CHES) buffer, tri s(hydroxymethyl)aminom ethane (Tris) buffer, or a N-cyclohexyl-3- aminopropanesulfonic acid (CAPS) buffer. In embodiments, the buffer is a borate buffer. In embodiments, the buffer is a CHES buffer. In embodiments, the sequencing reaction mixture includes nucleotides, wherein the nucleotides include a reversible terminating moiety and a label covalently linked to the nucleotide via a cleavable linker. In embodiments, the sequencing reaction mixture includes a buffer, DNA polymerase, detergent (e.g., Triton X), a chelator (e.g., EDTA), and/or salts (e.g., ammonium sulfate, magnesium chloride, sodium chloride, or potassium chloride).

[0071] As used herein, the term “sequencing cycle” is used in accordance with its plain and ordinary meaning and refers to incorporating one or more nucleotides (e.g., nucleotide analogues) to the 3’ end of a polynucleotide with a polymerase, and detecting one or more labels that identify the one or more nucleotides incorporated. In embodiments, one nucleotide (e.g., a modified nucleotide) is incorporated per sequencing cycle. The sequencing may be accomplished by, for example, sequencing by synthesis, pyrosequencing, and the like. In embodiments, a sequencing cycle includes extending a complementary polynucleotide by incorporating a first nucleotide using a polymerase, wherein the polynucleotide is hybridized to a template nucleic acid, detecting the first nucleotide, and identifying the first nucleotide. In embodiments, to begin a sequencing cycle, one or more differently labeled nucleotides and a DNA polymerase can be introduced. Following nucleotide addition, signals produced (e.g., via excitation and emission of a detectable label) can be detected to determine the identity of the incorporated nucleotide (based on the labels on the nucleotides). Reagents can then be added to remove the 3’ reversible terminator and to remove labels from each incorporated base. Reagents, enzymes, and other substances can be removed between steps by washing. Cycles may include repeating these steps, and the sequence of each cluster is read over the multiple repetitions.

[0072] As used herein, the term “extension” or “elongation” is used in accordance with their plain and ordinary meanings and refer to synthesis by a polymerase of a new polynucleotide strand complementary to a template strand by adding free nucleotides (e.g., dNTPs) from a reaction mixture that are complementary to the template in the 5’-to-3’ direction. Extension includes condensing the 5 ’-phosphate group of the dNTPs with the 3 ’-hydroxy group at the end of the nascent (elongating) DNA strand.

[0073] As used herein, the term “sequencing read” is used in accordance with its plain and ordinary meaning and refers to an inferred sequence of nucleotide bases (or nucleotide base probabilities) corresponding to all or part of a single polynucleotide fragment. A sequencing read may include 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, or more nucleotide bases. In embodiments, a sequencing read includes reading a barcode sequence and a template nucleotide sequence. In embodiments, a sequencing read includes reading a template nucleotide sequence. In embodiments, a sequencing read includes reading a barcode and not a template nucleotide sequence. Reads of length 20-40 base pairs (bp) are referred to as ultra-short. Typical sequencers produce read lengths in the range of 100-500 bp. Read length is a factor which can affect the results of biological studies. For example, longer read lengths improve the resolution of de novo genome assembly and detection of structural variants. In embodiments, a sequencing read includes reading a barcode and a template nucleotide sequence. In embodiments, a sequencing read includes reading a template nucleotide sequence. In embodiments, a sequencing read includes reading a barcode and not a template nucleotide sequence. In embodiments, a sequencing read includes a computationally derived string corresponding to the detected label. In some embodiments, a sequencing read may include 300, 400, 500, 600, 700, 800, 900, 1,000, 1,100, 1,200, 1,300, 1,400, 1,500, or more nucleotide bases.

[0074] The term “multiplexing” as used herein refers to an analytical method in which the presence and/or amount of multiple targets, e.g., multiple nucleic acid target sequences, can be assayed simultaneously by using the methods and devices as described herein, each of which has at least one different detection characteristic, e.g., fluorescence characteristic (for example excitation wavelength, emission wavelength, emission intensity, FWHM (full width at half maximum peak height), or fluorescence lifetime) or a unique nucleic acid or protein sequence characteristic. As used herein, the term “multiplex” is used to refer to an assay in which multiple (i.e. at least two) different biomolecules are assayed at the same time, and more particularly in the same aliquot of the sample, or in the same reaction mixture. In embodiments, more than two different biomolecules are assayed at the same time. In embodiments, at least 2, 4, 6, 8, 10, 20, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400 or 1500 or more biomolecules are detected according to the present method.

[0075] Complementary single stranded nucleic acids and/or substantially complementary single stranded nucleic acids can hybridize to each other under hybridization conditions, thereby forming a nucleic acid that is partially or fully double stranded. All or a portion of a nucleic acid sequence may be substantially complementary to another nucleic acid sequence, in some embodiments. As referred to herein, “substantially complementary” refers to nucleotide sequences that can hybridize with each other under suitable hybridization conditions. Hybridization conditions can be altered to tolerate varying amounts of sequence mismatch within complementary nucleic acids that are substantially complementary. Substantially complementary portions of nucleic acids that can hybridize to each other can be 75% or more, 76% or more, 77% or more, 78% or more, 79% or more, 80% or more, 81% or more, 82% or more, 83% or more, 84% or more, 85% or more, 86% or more, 87% or more, 88% or more, 89% or more, 90% or more, 91% or more, 92% or more, 93% or more, 94% or more, 95% or more, 96% or more, 97% or more, 98% or more or

99% or more complementary to each other. In some embodiments substantially complementary portions of nucleic acids that can hybridize to each other are 100% complementary. Nucleic acids, or portions thereof, that are configured to hybridize to each other often include nucleic acid sequences that are substantially complementary to each other.

[0076] “Hybridize” shall mean the annealing of a nucleic acid sequence to another nucleic acid sequence (e.g., one single-stranded nucleic acid (such as a primer) to another nucleic acid) based on the well-understood principle of sequence complementarity. In an embodiment the other nucleic acid is a single-stranded nucleic acid. In some embodiments, one portion of a nucleic acid hybridizes to itself, such as in the formation of a hairpin structure. The propensity for hybridization between nucleic acids depends on the temperature and ionic strength of their milieu, the length of the nucleic acids and the degree of complementarity. The effect of these parameters on hybridization is described in, for example, Sambrook J., Fritsch E. F., Maniatis T., Molecular cloning: a laboratory manual, Cold Spring Harbor Laboratory Press, New York (1989). As used herein, hybridization of a primer, or of a DNA extension product, respectively, is extendable by creation of a phosphodiester bond with an available nucleotide or nucleotide analogue capable of forming a phosphodiester bond, therewith. For example, hybridization can be performed at a temperature ranging from 15° C to 95° C. In some embodiments, the hybridization is performed at a temperature of about 20° C, about 25° C, about 30° C, about 35° C, about 40° C, about 45° C, about 50° C, about 55° C, about 60° C, about 65° C, about 70° C, about 75° C, about 80° C, about 85° C, about 90° C, or about 95° C. In other embodiments, the stringency of the hybridization can be further altered by the addition or removal of components of the buffered solution.

[0077] As used herein, “specifically hybridizes” refers to preferential hybridization under hybridization conditions where two nucleic acids, or portions thereof, that are substantially complementary, hybridize to each other and not to other nucleic acids that are not substantially complementary to either of the two nucleic acids. For example, specific hybridization includes the hybridization of a primer or capture nucleic acid to a portion of a target nucleic acid (e.g., a template, or adapter portion of a template) that is substantially complementary to the primer or capture nucleic acid. In some embodiments nucleic acids, or portions thereof, that are configured to specifically hybridize are often about 80% or more, 81% or more, 82% or more, 83% or more, 84% or more, 85% or more, 86% or more, 87% or more, 88% or more, 89% or more, 90% or more, 91% or more, 92% or more, 93% or more, 94% or more, 95% or more, 96% or more, 97% or more, 98% or more, 99% or more or 100% complementary to each other over a contiguous portion of nucleic acid sequence. A specific hybridization discriminates over non-specific hybridization interactions (e.g., two nucleic acids that a not configured to specifically hybridize, e.g., two nucleic acids that are 80% or less, 70% or less, 60% or less or 50% or less complementary) by about 2-fold or more, often about 10-fold or more, and sometimes about 1 GO- fold or more, 1000-fold or more, 10,000-fold or more, 100,000-fold or more, or 1,000,000-fold or more. Two nucleic acid strands that are hybridized to each other can form a duplex which includes a double stranded portion of nucleic acid.

[0078] As used herein, the term “adjacent,” refers to two nucleotide sequences in a nucleic acid, can refer to nucleotide sequences separated by 0 to about 20 nucleotides, more specifically, in a range of about 1 to about 10 nucleotides, or to sequences that directly abut one another. As those of skill in the art appreciate, two nucleotide sequences that that are to ligated together will generally directly abut one another.

[0079] A nucleic acid can be amplified by a suitable method. The term “amplification,” “amplified” or “amplifying” as used herein refers to subjecting a target nucleic acid in a sample to a process that linearly or exponentially generates amplicon nucleic acids having the same or substantially the same (e.g., substantially identical) nucleotide sequence as the target nucleic acid, or segment thereof, and/or a complement thereof (which may be referred to herein as an “amplification product” or “amplification products”). In some embodiments an amplification reaction includes a suitable thermal stable polymerase. Thermal stable polymerases are known and are stable for prolonged periods of time, at temperature greater than 80° C when compared to common polymerases found in most mammals. In certain embodiments the term “amplification,” “amplified” or “amplifying” refers to a method that includes a polymerase chain reaction (PCR). Conditions conducive to amplification (i.e., amplification conditions) are known and often include at least a suitable polymerase, a suitable template, a suitable primer or set of primers, suitable nucleotides (e.g., dNTPs), a suitable buffer, and application of suitable annealing, hybridization and/or extension times and temperatures. In certain embodiments an amplified product (e.g., an amplicon) can contain one or more additional and/or different nucleotides than the template sequence, or portion thereof, from which the amplicon was generated (e.g., a primer can contain “extra” nucleotides (such as a 5’ portion that does not hybridize to the template), or one or more mismatched bases within a hybridizing portion of the primer).

[0080] As used herein, bridge-PCR (bPCR) amplification is a method for solid-phase amplification as exemplified by the disclosures of U.S. Pat. Nos. 5,641,658; 7,115,400; and U.S. Patent Publ. No. 2008/0009420, each of which is incorporated herein by reference in its entirety. Bridge-PCR involves repeated polymerase chain reaction cycles, cycling between denaturation, annealing, and extension conditions and enables controlled, spatially-localized, amplification, to generate amplification products (e.g., amplicons) immobilized on a solid support in order to form arrays comprised of colonies (or “clusters”) of immobilized nucleic acid molecule. [0081] Amplification according to the present teachings encompasses any means by which at least a part of at least one target nucleic acid is reproduced, typically in a template-dependent manner, including without limitation, a broad range of techniques for amplifying nucleic acid sequences, either linearly or exponentially. Illustrative means for performing an amplifying step include ligase chain reaction (LCR), ligase detection reaction (LDR), ligation followed by Q- replicase amplification, PCR, primer extension, strand displacement amplification (SDA), hyperbranched strand displacement amplification, multiple displacement amplification (MDA), nucleic acid strand-based amplification (NASBA), two-step multiplexed amplifications, rolling circle amplification (RCA), and the like, including multiplex versions and combinations thereof, for example but not limited to, OLA (oligonucleotide ligation assay )/PCR, PCR/OLA, LDR/PCR, PCR/PCR/LDR, PCR/LDR, LCR/PCR, PCR/LCR (also known as combined chain reaction — CCR), and the like. Descriptions of such techniques can be found in, among other sources, Ausbel et al.; PCR Primer: A Laboratory Manual, Diffenbach, Ed., Cold Spring Harbor Press (1995); The Electronic Protocol Book, Chang Bioscience (2002); Msuih et al., J. Clin. Micro. 34:501-07 (1996); The Nucleic Acid Protocols Handbook, R. Rapley, ed., Humana Press, Totowa, N.J. (2002); Abramson et al., Curr Opin Biotechnol. 1993 February; 4(1):41 -7, U.S. Pat. Nos.

6,027,998; 6,605,451, Barany et al., PCT Publication No. WO 97/31256; Wenz et al., PCT Publication No. WO 01/92579; Day et al., Genomics, 29(1): 152-162 (1995), Ehrlich et al., Science 252: 1643-50 (1991); Innis et al., PCR Protocols: A Guide to Methods and Applications, Academic Press (1990); Favis et al., Nature Biotechnology 18:561-64 (2000); and Rabenau et al., Infection 28:97-102 (2000); Belgrader, Barany, and Lubin, Development of a Multiplex Ligation Detection Reaction DNA Typing Assay, Sixth International Symposium on Human Identification, 1995 (available on the world wide web at: promega.com/geneticidproc/ussymp6proc/blegrad.html-); LCR Kit Instruction Manual, Cat. #200520, Rev. #050002, Stratagene, 2002; Barany, Proc. Natl. Acad. Sci. USA 88: 188-93 (1991); Bi and Sambrook, Nucl. Acids Res. 25:2924-2951 (1997); Zirvi et al., Nucl. Acid Res. 27:e40i- viii (1999); Dean et al., Proc Natl Acad Sci USA 99:5261-66 (2002); Barany and Gelfand, Gene 109: 1-11 (1991); Walker et al., Nucl. Acid Res. 20: 1691-96 (1992); Polstra et al., BMC Inf. Dis. 2: 18-(2002); Lage et al., Genome Res. 2003 February; 13(2):294-307, and Landegren et al., Science 241 : 1077-80 (1988), Demidov, V., Expert Rev Mol Diagn. 2002 November; 2(6):542-8., Cook et al., J Microbiol Methods. 2003 May; 53(2): 165-74, Schweitzer et al., Curr Opin Biotechnol. 2001 February; 12(l):21-7, U.S. Pat. Nos. 5,830,711, 6,027,889, 5,686,243, PCT Publication No. WO0056927A3, and PCT Publication No. WO9803673A1. [0082] In some embodiments, amplification includes at least one cycle of the sequential procedures of annealing at least one primer with complementary or substantially complementary sequences in at least one target nucleic acid; synthesizing at least one strand of nucleotides in a template-dependent manner using a polymerase; and denaturing the newly-formed nucleic acid duplex to separate the strands. The cycle may or may not be repeated. Amplification can include thermocycling or can be performed isothermally.

[0083] As used herein, the term “rolling circle amplification (RCA)” refers to a nucleic acid amplification reaction that amplifies a circular nucleic acid template (e.g., single-stranded DNA circles) via a rolling circle mechanism. Rolling circle amplification reaction is initiated by the hybridization of a primer to a circular, often single-stranded, nucleic acid template. The nucleic acid polymerase then extends the primer that is hybridized to the circular nucleic acid template by continuously progressing around the circular nucleic acid template to replicate the sequence of the nucleic acid template over and over again (rolling circle mechanism). The rolling circle amplification typically produces concatemers including tandem repeat units of the circular nucleic acid template sequence. The rolling circle amplification may be a linear RCA (LRCA), exhibiting linear amplification kinetics (e.g., RCA using a single specific primer), or may be an exponential RCA (ERCA) exhibiting exponential amplification kinetics. Rolling circle amplification may also be performed using multiple primers (multiply primed rolling circle amplification or MPRCA) leading to hyper-branched concatemers. For example, in a double-primed RCA, one primer may be complementary, as in the linear RCA, to the circular nucleic acid template, whereas the other may be complementary to the tandem repeat unit nucleic acid sequences of the RCA product. Consequently, the double-primed RCA may proceed as a chain reaction with exponential (geometric) amplification kinetics featuring a ramifying cascade of multiple-hybridization, primer-extension, and strand-displacement events involving both the primers. This often generates a discrete set of concatemeric, double-stranded nucleic acid amplification products. The rolling circle amplification may be performed in-vitro under isothermal conditions using a suitable nucleic acid polymerase such as Phi29 DNA polymerase. RCA may be performed by using any of the DNA polymerases that are known in the art (e.g., a Phi29 DNA polymerase, a Bst DNA polymerase, or SD polymerase).

[0084] As used herein, the term “circularizing” refers to the conversion of a linear nucleic acid molecule into a circular form. Circularization of a linear nucleic acid molecule, such as DNA or RNA, involves covalently linking the two ends of the molecule together to form a closed circle. Circularization may be obtained by, for example, association of complementary single stranded ends (sticky ends). Circularization may also be obtained by ligating the two ends of the linear nucleic acids. The ligation can be blunt-end ligation or sticky-end ligation. Circularizing may also be facilitated by the use of a splint oligonucleotide. For example, the two ends of a linear nucleic acid molecule are hybridized to two regions of a splint oligonucleotide such that the ends (i.e., the 5’ and 3’ ends) of the linear nucleic acid molecule are adjacent to each other, and a ligase is then used, for example, to covalently link the two ends together.

[0085] A nucleic acid can be amplified by a thermocycling method or by an isothermal amplification method. In some embodiments a rolling circle amplification method is used. In some embodiments amplification takes place on a solid support (e.g., within a flow cell) where a nucleic acid, nucleic acid library or portion thereof is immobilized. In certain sequencing methods, a nucleic acid library is added to a flow cell and immobilized by hybridization to anchors under suitable conditions. This type of nucleic acid amplification is often referred to as solid phase amplification. In some embodiments of solid phase amplification, all or a portion of the amplified products are synthesized by an extension initiating from an immobilized primer. Solid phase amplification reactions are analogous to standard solution phase amplifications except that at least one of the amplification oligonucleotides (e.g., primers) is immobilized on a solid support.

[0086] In some embodiments solid phase amplification includes a nucleic acid amplification reaction including only one species of oligonucleotide primer immobilized to a surface or substrate. In certain embodiments solid phase amplification includes a plurality of different immobilized oligonucleotide primer species. In some embodiments solid phase amplification may include a nucleic acid amplification reaction including one species of oligonucleotide primer immobilized on a solid surface and a second different oligonucleotide primer species in solution. Multiple different species of immobilized or solution-based primers can be used. Non-limiting examples of solid phase nucleic acid amplification reactions include interfacial amplification, bridge PCR amplification, emulsion PCR, WildFire amplification (e.g., US patent publication US20130012399), the like or combinations thereof.

[0087] As used herein, the terms “cluster” and “colony” are used interchangeably to refer to a discrete site on a solid support that includes a plurality of immobilized polynucleotides and a plurality of immobilized complementary polynucleotides. The term “clustered array” refers to an array formed from such clusters or colonies. In this context the term “array” is not to be understood as requiring an ordered arrangement of clusters. The term “array” is used in accordance with its ordinary meaning in the art, and refers to a population of different molecules that are attached to one or more solid-phase substrates such that the different molecules can be differentiated from each other according to their relative location. An array can include different molecules that are each located at different addressable features on a solid-phase substrate. The molecules of the array can be nucleic acid primers, nucleic acid probes, nucleic acid templates or nucleic acid enzymes such as polymerases or ligases. Arrays useful in the invention can have densities that ranges from about 2 different features to many millions, billions or higher. The density of an array can be from 2 to as many as a billion or more different features per square cm. For example an array can have at least about 100 features/cm², at least about 1,000 features/cm², at least about 10,000 features /cm², at least about 100,000 features /cm², at least about 10,000,000 features /cm², at least about 100,000,000 features /cm², at least about 1,000,000,000 features /cm², at least about 2,000,000,000 features /cm² or higher. In embodiments, the arrays have features at any of a variety of densities including, for example, at least about 10 features/cm², 100 features/cm², 500 features/cm², 1,000 features/cm², 5,000 features/cm², 10,000 features/cm², 50,000 features/cm², 100,000 features/cm², 1,000,000 features/cm², 5,000,000 features/cm², or higher.

[0088] Provided herein are methods, systems, and compositions for analyzing a sample (e.g., sequencing nucleic acids within a sample) in situ. The term “in situ" is used in accordance with its ordinary meaning in the art and refers to a sample surrounded by at least a portion of its native environment, such as may preserve the relative position of two or more elements. For example, an extracted human cell obtained is considered in situ when the cell is retained in its local microenvironment so as to avoid extracting the target (e.g., nucleic acid molecules or proteins) away from their native environment. An in situ sample (e.g., a cell) can be obtained from a suitable subject. An in situ cell sample may refer to a cell and its surrounding milieu, or a tissue. A sample can be isolated or obtained directly from a subject or part thereof. In embodiments, the methods described herein (e.g., sequencing a plurality of target nucleic acids of a cell in situ) are applied to an isolated cell (i.e., a cell not surrounded by least a portion of its native environment). For the avoidance of any doubt, when the method is performed within a cell (e.g., an isolated cell) the method may be considered in situ. In some embodiments, a sample is obtained indirectly from an individual or medical professional. A sample can be any specimen that is isolated or obtained from a subject or part thereof. A sample can be any specimen that is isolated or obtained from multiple subjects. Non-limiting examples of specimens include fluid or tissue from a subject, including, without limitation, blood or a blood product (e.g., serum, plasma, platelets, buffy coats, or the like), umbilical cord blood, chorionic villi, amniotic fluid, cerebrospinal fluid, spinal fluid, lavage fluid (e.g., lung, gastric, peritoneal, ductal, ear, arthroscopic), a biopsy sample, celocentesis sample, cells (blood cells, lymphocytes, placental cells, stem cells, bone marrow derived cells, embryo or fetal cells) or parts thereof (e.g., mitochondrial, nucleus, extracts, or the like), urine, feces, sputum, saliva, nasal mucous, prostate fluid, lavage, semen, lymphatic fluid, bile, tears, sweat, breast milk, breast fluid, the like or combinations thereof. Non-limiting examples of tissues include organ tissues (e.g., liver, kidney, lung, thymus, adrenals, skin, bladder, reproductive organs, intestine, colon, spleen, brain, the like or parts thereof), epithelial tissue, hair, hair follicles, ducts, canals, bone, eye, nose, mouth, throat, ear, nails, the like, parts thereof or combinations thereof. A sample may include cells or tissues that are normal, healthy, diseased (e.g., infected), and/or cancerous (e.g., cancer cells). A sample obtained from a subject may include cells or cellular material (e.g., nucleic acids) of multiple organisms (e.g., virus nucleic acid, fetal nucleic acid, bacterial nucleic acid, parasite nucleic acid). A sample may include a cell and RNA transcripts. A sample can include nucleic acids obtained from one or more subjects. In some embodiments a sample includes nucleic acid obtained from a single subject. A subject can be any living or non-living organism, including but not limited to a human, nonhuman animal, plant, bacterium, fungus, virus, or protist. A subject may be any age (e.g., an embryo, a fetus, infant, child, adult). A subject can be of any sex (e.g., male, female, or combination thereof). A subject may be pregnant. In some embodiments, a subject is a mammal. In some embodiments, a subject is a plant. In some embodiments, a subject is a human subject. A subject can be a patient (e.g., a human patient). In some embodiments a subject is suspected of having a genetic variation or a disease or condition associated with a genetic variation.

[0089] As used herein, the term “disease state” is used in accordance with its plain and ordinary meaning and refers to any abnormal biological or aberrant state of a cell. The presence of a disease state may be identified by the same collection of biological constituents used to determine the cell’s biological state. In general, a disease state will be detrimental to a biological system. A disease state may be a consequence of, inter alia, an environmental pathogen, for example a viral infection (e.g., HIV/AIDS, hepatitis B, hepatitis C, influenza, measles, etc.), a bacterial infection, a parasitic infection, a fungal infection, or infection by some other organism. A disease state may also be the consequence of some other environmental agent, such as a chemical toxin or a chemical carcinogen. As used herein, a disease state further includes genetic disorders wherein one or more copies of a gene is altered or disrupted, thereby affecting its biological function. Exemplary genetic diseases include, but are not limited to polycystic kidney disease, familial multiple endocrine neoplasia type I, neurofibromatoses, Tay-Sachs disease, Huntington’s disease, sickle cell anemia, thalassemia, and Down’s syndrome, as well as others (see, e.g., The Metabolic and Molecular Bases of Inherited Diseases, 7th ed., McGraw-Hill Inc., New York). Other exemplary diseases include, but are not limited to, cancer, hypertension, Alzheimer’s disease, neurodegenerative diseases, and neuropsychiatric disorders such as bipolar affective disorders or paranoid schizophrenic disorders. Disease states are monitored to determine the level or severity (e.g., the stage or progression) of one or more disease states of a subject and, more specifically, detect changes in the biological state of a subject which are correlated to one or more disease states (see, e.g., U.S. Pat. No. 6,218,122, which is incorporated by reference herein in its entirety). In embodiments, methods provided herein are also applicable to monitoring the disease state or states of a subject undergoing one or more therapies. Thus, the present disclosure also provides, in some embodiments, methods for determining or monitoring efficacy of a therapy or therapies (i.e., determining a level of therapeutic effect) upon a subject. In embodiments, methods of the present disclosure can be used to assess therapeutic efficacy in a clinical trial, e.g., as an early surrogate marker for success or failure in such a clinical trial. Within eukaryotic cells, there are hundreds to thousands of signaling pathways that are interconnected. For this reason, perturbations in the function of proteins within a cell have numerous effects on other proteins and the transcription of other genes that are connected by primary, secondary, and sometimes tertiary pathways. This extensive interconnection between the function of various proteins means that the alteration of any one protein is likely to result in compensatory changes in a wide number of other proteins. In particular, the partial disruption of even a single protein within a cell, such as by exposure to a drug or by a disease state which modulates the gene copy number (e.g., a genetic mutation), results in characteristic compensatory changes in the transcription of enough other genes that these changes in transcripts can be used to define a “signature” of particular transcript alterations which are related to the disruption of function, e.g., a particular disease state or therapy, even at a stage where changes in protein activity are undetectable.

[0090] The terms “polypeptide,” “peptide” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues, wherein the polymer may optionally be conjugated to a moiety that does not consist of amino acids. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers and non-naturally occurring amino acid polymer. A protein may refer to a protein expressed in a cell.

[0091] A polypeptide, or a cell is “recombinant” when it is artificial or engineered, or derived from or contains an artificial or engineered protein or nucleic acid (e.g., non-natural or not wild type). For example, a polynucleotide that is inserted into a vector or any other heterologous location, e.g., in a genome of a recombinant organism, such that it is not associated with nucleotide sequences that normally flank the polynucleotide as it is found in nature is a recombinant polynucleotide. A protein expressed in vitro or in vivo from a recombinant polynucleotide is an example of a recombinant polypeptide. Likewise, a polynucleotide sequence that does not appear in nature, for example a variant of a naturally occurring gene, is recombinant.

[0092] As used herein, a “single cell” refers to one cell. Single cells useful in the methods described herein can be obtained from a tissue of interest, or from a biopsy, blood sample, or cell culture. Additionally, cells from specific organs, tissues, tumors, neoplasms, or the like can be obtained and used in the methods described herein. In general, cells from any population can be used in the methods, such as a population of prokaryotic or eukaryotic organisms, including bacteria or yeast.

[0093] The term “cellular component” is used in accordance with its ordinary meaning in the art and refers to any organelle, nucleic acid, protein, or analyte that is found in a prokaryotic, eukaryotic, archaeal, or other organismic cell type. Examples of cellular components (e.g., a component of a cell) include RNA transcripts, proteins, membranes, lipids, and other analytes.

[0094] A “gene” refers to a polynucleotide that is capable of conferring biological function after being transcribed and/or translated.

[0095] As used herein, the terms “biomolecule” or “analyte” refer to an agent (e.g., a compound, macromolecule, or small molecule), and the like derived from a biological system (e.g., an organism, a cell, or a tissue). The biomolecule may contain multiple individual components that collectively construct the biomolecule, for example, in embodiments, the biomolecule is a polynucleotide wherein the polynucleotide is composed of nucleotide monomers. The biomolecule may be or may include DNA, RNA, organelles, carbohydrates, lipids, proteins, or any combination thereof. These components may be extracellular. In some examples, the biomolecule may be referred to as a clump or aggregate of combinations of components. In some instances, the biomolecule may include one or more constituents of a cell but may not include other constituents of the cell. In embodiments, a biomolecule is a molecule produced by a biological system (e.g., an organism). The biomolecule may be any substance (e.g. molecule) or entity that is desired to be detected by the method of the invention. In embodiments, the biomolecule is the “target” of the assay methods describred herein. The biomolecule may accordingly be any compound that may be desired to be detected, for example a peptide or protein, or nucleic acid molecule or a small molecule, including organic and inorganic molecules. The biomolecule may be a cell or a microorganism, including a virus, or a fragment or product thereof. Biomolecules of particular interest may thus include proteinaceous molecules such as peptides, polypeptides, proteins or prions or any molecule which includes a protein or polypeptide component, etc., or fragments thereof. The biomolecule may be a single molecule or a complex that contains two or more molecular subunits, which may or may not be be covalently bound to one another, and which may be the same or different. Thus, in addition to cells or microorganisms, such a complex biomolecule may also be a protein complex. Such a complex may thus be a homo- or hetero-multimer. Aggregates of molecules e.g., proteins may also be target analytes, for example aggregates of the same protein or different proteins. The biomolecule may also be a complex between proteins or peptides and nucleic acid molecules such as DNA or RNA. Of particular interest may be the interactions between proteins and nucleic acids, e.g., regulatory factors, such as transcription factors, and interactions between DNA or RNA molecules

[0096] As used herein, “biomaterial” refers to any biological material produced by an organism. In some embodiments, biomaterial includes secretions, extracellular matrix, proteins, lipids, organelles, membranes, cells, portions thereof, and combinations thereof. In some embodiments, cellular material includes secretions, extracellular matrix, proteins, lipids, organelles, membranes, cells, portions thereof, and combinations thereof. In some embodiments, biomaterial includes viruses. In some embodiments, the biomaterial is a replicating virus and thus includes virus infected cells. In embodiments, a biological sample includes biomaterials.

[0097] In some embodiments, a sample includes one or more nucleic acids, or fragments thereof. A sample can include nucleic acids obtained from one or more subjects. In some embodiments a sample includes nucleic acid obtained from a single subject. In some embodiments, a sample includes a mixture of nucleic acids. A mixture of nucleic acids can include two or more nucleic acid species having different nucleotide sequences, different fragment lengths, different origins (e.g., genomic origins, cell or tissue origins, subject origins, the like or combinations thereof), or combinations thereof. A sample may include synthetic nucleic acid.

[0098] A subject can be any living or non-living organism, including but not limited to a human, non-human animal, plant, bacterium, fungus, virus or protist. A subject may be any age (e.g., an embryo, a fetus, infant, child, adult). A subject can be of any sex (e.g., male, female, or combination thereof). A subject may be pregnant. In some embodiments, a subject is a mammal. In some embodiments, a subject is a human subject. A subject can be a patient (e.g., a human patient). In some embodiments a subject is suspected of having a genetic variation or a disease or condition associated with a genetic variation.

[0099] The methods and kits of the present disclosure may be applied, mutatis mutandis, to the sequencing of RNA, or to determining the identity of a ribonucleotide. [0100] As used herein, the term “kit” refers to any delivery system for delivering materials. In the context of reaction assays, such delivery systems include systems that allow for the storage, transport, or delivery of reaction reagents (e.g., oligonucleotides, enzymes, etc. in the appropriate containers) and/or supporting materials (e.g., packaging, buffers, written instructions for performing a method, etc.) from one location to another. For example, kits include one or more enclosures (e.g., boxes) containing the relevant reaction reagents and/or supporting materials. As used herein, the term “fragmented kit” refers to a delivery system including two or more separate containers that each contain a subportion of the total kit components. The containers may be delivered to the intended recipient together or separately. For example, a first container may contain an enzyme for use in an assay, while a second container contains oligonucleotides. In contrast, a “combined kit” refers to a delivery system containing all of the components of a reaction assay in a single container (e.g., in a single box housing each of the desired components). The term “kit” includes both fragmented and combined kits.

[0101] As used herein the term “determine” can be used to refer to the act of ascertaining, establishing or estimating. A determination can be probabilistic. For example, a determination can have an apparent likelihood of at least 50%, 75%, 90%, 95%, 98%, 99%, 99.9% or higher. In some cases, a determination can have an apparent likelihood of 100%. An exemplary determination is a maximum likelihood analysis or report. As used herein, the term “identify,” when used in reference to a thing, can be used to refer to recognition of the thing, distinction of the thing from at least one other thing or categorization of the thing with at least one other thing. The recognition, distinction or categorization can be probabilistic. For example, a thing can be identified with an apparent likelihood of at least 50%, 75%, 90%, 95%, 98%, 99%, 99.9% or higher. A thing can be identified based on a result of a maximum likelihood analysis. In some cases, a thing can be identified with an apparent likelihood of 100%.

[0102] The terms “bioconjugate group,” “bioconjugate reactive moiety,” and “bioconjugate reactive group” refer to a chemical moiety which participates in a reaction to form a bioconjugate linker (e.g., covalent linker). Non-limiting examples of bioconjugate reactive groups and the resulting bioconjugate reactive linkers may be found in the Bioconjugate Table below:

Bioconjugate reactive group 1 Bioconjugate reactive group 2 Resulting Bioconjugate (e.g., electrophilic (e.g., nucleophilic bioconjugate reactive linker bioconjugate reactive moiety) reactive moiety) activated esters amines/anilines carboxamides acrylamides thiols thioethers acyl azides amines/anilines carboxamides acyl halides amines/anilines carboxamides acyl halides alcohols/phenols esters Bioconjugate reactive group 1 Bioconjugate reactive group 2 Resulting Bioconjugate (e.g., electrophilic (e.g., nucleophilic bioconjugate reactive linker bioconjugate reactive moiety) reactive moiety) acyl nitriles alcohols/phenols esters acyl nitriles amines/anilines carboxamides aldehydes amines/anilines imines aldehydes or ketones hydrazines hydrazones aldehydes or ketones hydroxylamines oximes alkyl halides amines/anilines alkyl amines alkyl halides carboxylic acids esters alkyl halides thiols thioethers alkyl halides alcohols/phenols ethers alkyl sulfonates thiols thioethers alkyl sulfonates carboxylic acids esters alkyl sulfonates alcohols/phenols ethers anhydrides alcohols/phenols esters anhydrides amines/anilines carboxamides aryl halides thiols thiophenols aryl halides amines aryl amines aziridines thiols thioethers boronates glycols boronate esters carbodiimides carboxylic acids N-acylureas or anhydrides diazoalkanes carboxylic acids esters epoxides thiols thioethers haloacetamides thiols thioethers haloplatinate amino platinum complex haloplatinate heterocycle platinum complex haloplatinate thiol platinum complex halotriazines amines/anilines aminotriazines halotriazines alcohols/phenols triazinyl ethers halotriazines thiols triazinyl thioethers imido esters amines/anilines amidines isocyanates amines/anilines ureas isocyanates alcohols/phenols urethanes isothiocyanates amines/anilines thioureas maleimides thiols thioethers phosphoramidites alcohols phosphite esters silyl halides alcohols silyl ethers sulfonate esters amines/anilines alkyl amines sulfonate esters thiols thioethers sulfonate esters carboxylic acids esters sulfonate esters alcohols ethers sulfonyl halides amines/anilines sulfonamides sulfonyl halides phenols/alcohols sulfonate esters

[0103] As used herein, the term “bioconjugate reactive moiety” and “bioconjugate reactive group” refers to a moiety or group capable of forming a bioconjugate (e.g., covalent linker) as a result of the association between atoms or molecules of bioconjugate reactive groups. The association can be direct or indirect. For example, a conjugate between a first bioconjugate reactive group (e.g., -NH2, -COOH, -N-hydroxysuccinimide, or -maleimide) and a second bioconjugate reactive group (e.g., sulfhydryl, sulfur-containing amino acid, amine, amine sidechain containing amino acid, or carboxylate) provided herein can be direct, e.g., by covalent bond or linker (e.g., a first linker of second linker), or indirect, e.g., by non-covalent bond (e.g., electrostatic interactions (e.g., ionic bond, hydrogen bond, halogen bond), van der Waals interactions (e.g., dipole-dipole, dipole-induced dipole, London dispersion), ring stacking (pi effects), hydrophobic interactions and the like). In embodiments, bioconjugates or bioconjugate linkers are formed using bioconjugate chemistry (i.e., the association of two bioconjugate reactive groups) including, but are not limited to nucleophilic substitutions (e.g., reactions of amines and alcohols with acyl halides, active esters), electrophilic substitutions (e.g., enamine reactions) and additions to carbon-carbon and carbon-heteroatom multiple bonds (e.g., Michael reaction, Diels- Alder addition). These and other useful reactions are discussed in, for example, March, ADVANCED ORGANIC CHEMISTRY, 3rd Ed., John Wiley & Sons, New York, 1985; Hermanson, BIOCONJUGATE TECHNIQUES, Academic Press, San Diego, 1996; and Feeney et al.. MODIFICATION OF PROTEINS; Advances in Chemistry Series, Vol. 198, American Chemical Society, Washington, D.C., 1982. In embodiments, the first bioconjugate reactive group (e.g., maleimide moiety) is covalently attached to the second bioconjugate reactive group (e.g., a sulfhydryl). In embodiments, the first bioconjugate reactive group (e.g., haloacetyl moiety) is covalently attached to the second bioconjugate reactive group (e.g., a sulfhydryl). In embodiments, the first bioconjugate reactive group (e.g., pyridyl moiety) is covalently attached to the second bioconjugate reactive group (e.g., a sulfhydryl). In embodiments, the first bioconjugate reactive group (e.g., -N-hydroxysuccinimide moiety) is covalently attached to the second bioconjugate reactive group (e.g., an amine). In embodiments, the first bioconjugate reactive group (e.g., maleimide moiety) is covalently attached to the second bioconjugate reactive group (e.g., a sulfhydryl). In embodiments, the first bioconjugate reactive group (e.g., -sulfo-N- hydroxysuccinimide moiety) is covalently attached to the second bioconjugate reactive group (e.g., an amine).

[0104] Useful bioconjugate reactive groups used for bioconjugate chemistries herein include, for example: (a) carboxyl groups and various derivatives thereof including, but not limited to, N- hydroxysuccinimide esters, N-hydroxybenztriazole esters, acid halides, acyl imidazoles, thioesters, p-nitrophenyl esters, alkyl, alkenyl, alkynyl and aromatic esters; (b) hydroxyl groups which can be converted to esters, ethers, aldehydes, etc.; (c) haloalkyl groups wherein the halide can be later displaced with a nucleophilic group such as, for example, an amine, a carboxylate anion, thiol anion, carbanion, or an alkoxide ion, thereby resulting in the covalent attachment of a new group at the site of the halogen atom; (d) dienophile groups which are capable of participating in Diels- Alder reactions such as, for example, maleimido or maleimide groups; (e) aldehyde or ketone groups such that subsequent derivatization is possible via formation of carbonyl derivatives such as, for example, imines, hydrazones, semicarbazones or oximes, or via such mechanisms as Grignard addition or alkyllithium addition; (f) sulfonyl halide groups for subsequent reaction with amines, for example, to form sulfonamides; (g) thiol groups, which can be converted to disulfides, reacted with acyl halides, or bonded to metals such as gold, or react with maleimides; (h) amine or sulfhydryl groups (e.g., present in cysteine), which can be, for example, acylated, alkylated or oxidized;(i) alkenes, which can undergo, for example, cycloadditions, acylation, Michael addition, etc.; (j) epoxides, which can react with, for example, amines and hydroxyl compounds; (k) phosphoramidites and other standard functional groups useful in nucleic acid synthesis; (1) metal silicon oxide bonding; (m) metal bonding to reactive phosphorus groups (e.g., phosphines) to form, for example, phosphate diester bonds.; (n) azides coupled to alkynes using copper catalyzed cycloaddition click chemistry; (o) biotin conjugate can react with avidin or strepavidin to form a avidin-biotin complex or streptavidin-biotin complex.

[0105] An “antibody” (Ab) is a protein that binds specifically to a particular substance, known as an “antigen” (Ag). An “antibody” or “antigen-binding fragment” is an immunoglobulin that binds a specific “epitope.” The term encompasses polyclonal, monoclonal, and chimeric antibodies. In nature, antibodies are generally produced by lymphocytes in response to immune challenge, such as by infection or immunization. An “antigen” (Ag) is any substance that reacts specifically with antibodies or T lymphocytes (T cells). An antibody may include the entire antibody as well as any antibody fragments capable of binding the antigen or antigenic fragment of interest. Examples include complete antibody molecules, antibody fragments, such as Fab, F(ab’)2, CDRs, VL, VH, and any other portion of an antibody which is capable of specifically binding to an antigen. Antibodies used herein are immunospecific for, and therefore specifically and selectively bind to, for example, proteins either detected (e.g., biological targets of interest) or used for detection (e.g., probes containing oligonucleotide barcodes) in the methods and devices as described herein.

[0106] The term “covalent linker” is used in accordance with its ordinary meaning and refers to a divalent moiety which connects at least two moieties to form a molecule.

[0107] The term “non-covalent linker” is used in accordance with its ordinary meaning and refers to a divalent moiety which includes at least two molecules that are not covalently linked to each other but are capable of interacting with each other via a non-covalent bond (e.g., electrostatic interactions (e.g., ionic bond, hydrogen bond, halogen bond) or van der Waals interactions (e.g., dipole-dipole, dipole-induced dipole, London dispersion). In embodiments, the non-covalent linker is the result of two molecules that are not covalently linked to each other that interact with each other via a non-covalent bond.

[0108] As used herein a “genetically modifying agent” is a substance that alters the genetic sequence of a cell following exposure to the cell, resulting in an agent-mediated nucleic acid sequence. In embodiments, the genetically modifying agent is a small molecule, protein, pathogen (e.g., virus or bacterium), toxin, oligonucleotide, or antigen. In embodiments, the genetically modifying agent is a virus (e.g., influenza) and the agent-mediated nucleic acid sequence is the nucleic acid sequence that develops within a T-cell upon cellular exposure and contact with the virus. In embodiments, the genetically modifying agent modulates the expression of a nucleic acid sequence in a cell relative to a control (e.g., the absence of the genetically modifying agent).

[0109] Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly indicates otherwise, between the upper and lower limit of that range, and any other stated or unstated intervening value in, or smaller range of values within, that stated range is encompassed within the invention. The upper and lower limits of any such smaller range (within a more broadly recited range) may independently be included in the smaller ranges, or as particular values themselves, and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention.

[0110] As used herein, the term “upstream” refers to a region in the nucleic acid sequence that is towards the 5’ end of a particular reference point, and the term “downstream” refers to a region in the nucleic acid sequence that is toward the 3’ end of the reference point.

[OHl] As used herein, the terms “incubate,” and “incubation refer collectively to altering the temperature of an object in a controlled manner such that conditions are sufficient for conducting the desired reaction. Thus, it is envisioned that the terms encompass heating a receptacle (e.g., a microplate) to a desired temperature and maintaining such temperature for a fixed time interval. Also included in the terms is the act of subjecting a receptacle to one or more heating and cooling cycles (i.e., “temperature cycling” or “thermal cycling”). While temperature cycling typically occurs at relatively high rates of change in temperature, the term is not limited thereto, and may encompass any rate of change in temperature.

[0112] As used herein, “biological activity” may include the in vivo activities of a compound or physiological responses that result upon in vivo administration of a compound, composition or other mixture. Biological activity, thus, may encompass therapeutic effects and pharmaceutical activity of such compounds, compositions and mixtures. Biological activities may be observed in vitro systems designed to test or use such activities.

[0113] The term “isolated” means altered or removed from the natural state. For example, a nucleic acid or a polypeptide naturally present in a living animal is not isolated, but the same nucleic acid or polypeptide partially or completely separated from the coexisting materials of its natural state is isolated. An isolated nucleic acid or protein can exist in substantially purified form, or can exist in a non-native environment such as, for example, a host cell. In embodiments, “isolated” refers to a nucleic acid, polynucleotide, polypeptide, protein, or other component that is partially or completely separated from components with which it is normally associated (other proteins, nucleic acids, cells, etc.).

[0114] The term “synthetic target” as used herein refers to a modified protein or nucleic acid such as those constructed by synthetic methods. In embodiments, a synthetic target is artificial or engineered, or derived from or contains an artificial or engineered protein or nucleic acid (e.g., non-natural or not wild type). For example, a polynucleotide that is inserted or removed such that it is not associated with nucleotide sequences that normally flank the polynucleotide as it is found in nature is a synthetic target polynucleotide.

[0115] The term “nucleic acid sequencing device” and the like means an integrated system of one or more chambers, ports, and channels that are interconnected and in fluid communication and designed for carrying out an analytical reaction or process, either alone or in cooperation with an appliance or instrument that provides support functions, such as sample introduction, fluid and/or reagent driving means, temperature control, detection systems, data collection and/or integration systems, for the purpose of determining the nucleic acid sequence of a template polynucleotide. Nucleic acid sequencing devices may further include valves, pumps, and specialized functional coatings on interior walls. Nucleic acid sequencing devices may include a receiving unit, or platen, that orients the flow cell such that a maximal surface area of the flow cell is available to be exposed to an optical lens. Other nucleic acid sequencing devices include those provided by Singular Genomics® (e.g., the G4® system), Illumina™ (e.g., HiSeq™, MiSeq™, NextSeq™, or NovaSeq™ systems), Life Technologies™ (e.g., ABI PRISM™, or SOLiD™ systems), Pacific Biosciences (e.g., systems using SMRT™ Technology such as the Sequel™ or RS II™ systems), or Qiagen (e.g., Genereader™ system). Nucleic acid sequencing devices may further include fluidic reservoirs (e.g., bottles), valves, pressure sources, pumps, sensors, control systems, valves, pumps, and specialized functional coatings on interior walls. In embodiments, the device includes a plurality of a sequencing reagent reservoirs and a plurality of clustering reagent reservoirs. In embodiments, the clustering reagent reservoir includes amplification reagents (e.g., an aqueous buffer containing enzymes, salts, and nucleotides, denaturants, crowding agents, etc.) In embodiments, the reservoirs include sequencing reagents (such as an aqueous buffer containing enzymes, salts, and nucleotides); a wash solution (an aqueous buffer); a cleave solution (an aqueous buffer containing a cleaving agent, such as a reducing agent); or a cleaning solution (a dilute bleach solution, dilute NaOH solution, dilute HC1 solution, dilute antibacterial solution, or water). The fluid of each of the reservoirs can vary. The fluid can be, for example, an aqueous solution which may contain buffers (e.g., saline-sodium citrate (SSC), ascorbic acid, tri s(hydroxymethyl)aminom ethane or “Tris”), aqueous salts (e.g., KC1 or (NHThSCh)), nucleotides, polymerases, cleaving agent (e.g., tri-n-butyl-phosphine, triphenyl phosphine and its sulfonated versions (i.e., tris(3-sulfophenyl)-phosphine, TPPTS), and tri(carboxyethyl)phosphine (TCEP) and its salts, cleaving agent scavenger compounds (e.g., 2'- Dithiobisethanamine or 1 l-Azido-3,6,9- tri oxaundecane- 1 -amine), chelating agents (e.g., EDTA), detergents, surfactants, crowding agents, or stabilizers (e.g., PEG, Tween, BSA). Non-limited examples of reservoirs include cartridges, pouches, vials, containers, and eppendorf tubes. In embodiments, the device is configured to perform fluorescent imaging. In embodiments, the device includes one or more light sources (e.g., one or more lasers). In embodiments, the illuminator or light source is a radiation source (i.e., an origin or generator of propagated electromagnetic energy) providing incident light to the sample. A radiation source can include an illumination source producing electromagnetic radiation in the ultraviolet (UV) range (about 200 to 390 nm), visible (VIS) range (about 390 to 770 nm), or infrared (IR) range (about 0.77 to 25 microns), or other range of the electromagnetic spectrum. In embodiments, the illuminator or light source is a lamp such as an arc lamp or quartz halogen lamp. In embodiments, the illuminator or light source is a coherent light source. In embodiments, the light source is a laser, LED (light emitting diode), a mercury or tungsten lamp, or a super-continuous diode. In embodiments, the light source provides excitation beams having a wavelength between 200 nm to 1500 nm. In embodiments, the laser provides excitation beams having a wavelength of 405 nm, 470 nm, 488 nm, 514 nm, 520 nm, 532 nm, 561 nm, 633 nm, 639 nm, 640 nm, 800 nm, 808 nm, 912 nm, 1024 nm, or 1500 nm. In embodiments, the illuminator or light source is a light-emitting diode (LED). The LED can be, for example, an Organic Light Emitting Diode (OLED), a Thin Film Electroluminescent Device (TFELD), or a Quantum dot based inorganic organic LED. The LED can include a phosphorescent OLED (PHOLED). In embodiments, the nucleic acid sequencing device includes an imaging system (e.g., an imaging system as described herein). The imaging system capable of exciting one or more of the identifiable labels (e.g., a fluorescent label) linked to a nucleotide and thereafter obtain image data for the identifiable labels. The image data (e.g., detection data) may be analyzed by another component within the device. The imaging system may include a system described herein and may include a fluorescence spectrophotometer including an objective lens and/or a solid-state imaging device. The solid-state imaging device may include a charge coupled device (CCD) and/or a complementary metal oxide semiconductor (CMOS). The system may also include circuitry and processors, including systems using microcontrollers, reduced instruction set computers (RISC), application specific integrated circuits (ASICs), field programmable gate array (FPGAs), logic circuits, and any other circuit or processor capable of executing functions described herein. The set of instructions may be in the form of a software program. As used herein, the terms “software” and “firmware” are interchangeable, and include any computer program stored in memory for execution by a computer, including RAM memory, ROM memory, EPROM memory, EEPROM memory, and non-volatile RAM (NVRAM) memory. In embodiments, the device includes a thermal control assembly useful to control the temperature of the reagents.

[0116] The term “image” is used according to its ordinary meaning and refers to a representation of all or part of an object. The representation may be an optically detected reproduction. For example, an image can be obtained from fluorescent, luminescent, scatter, or absorption signals. The part of the object that is present in an image can be the surface or other xy plane of the object. Typically, an image is a 2 dimensional representation of a 3 dimensional object. An image may include signals at differing intensities (i.e., signal levels). An image can be provided in a computer readable format or medium. An image is derived from the collection of focus points of light rays coming from an object (e.g., the sample), which may be detected by any image sensor.

[0117] As used herein, the term “signal” is intended to include, for example, fluorescent, luminescent, scatter, or absorption impulse or electromagnetic wave transmitted or received. Signals can be detected in the ultraviolet (UV) range (about 200 to 390 nm), visible (VIS) range (about 391 to 770 nm), infrared (IR) range (about 0.771 to 25 microns), or other range of the electromagnetic spectrum. The term “signal level” refers to an amount or quantity of detected energy or coded information. For example, a signal may be quantified by its intensity, wavelength, energy, frequency, power, luminance, or a combination thereof. Other signals can be quantified according to characteristics such as voltage, current, electric field strength, magnetic field strength, frequency, power, temperature, etc. Absence of signal is understood to be a signal level of zero or a signal level that is not meaningfully distinguished from noise. [0118] The term “xy coordinates” refers to information that specifies location, size, shape, and/or orientation in an xy plane. The information can be, for example, numerical coordinates in a Cartesian system. The coordinates can be provided relative to one or both of the x and y axes or can be provided relative to another location in the xy plane (e.g., a fiducial). The term “xy plane” refers to a 2 dimensional area defined by straight line axes x and y. When used in reference to a detecting apparatus and an object observed by the detector, the xy plane may be specified as being orthogonal to the direction of observation between the detector and object being detected.

[0119] As used herein, the term “tissue section” refers to a piece of tissue that has been obtained from a subject, optionally fixed and attached to a surface, e.g., a microscope slide.

[0120] It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims. All publications, patents, and patent applications cited herein are hereby incorporated by reference in their entirety for all purposes.

II. Compositions & Kits

[0121] In an aspect is provided a complex including: i) a circular polynucleotide including a probe sequence, a target hybridization sequence, a subject sequence complement, and a target sequence complement; and ii) a splint oligonucleotide hybridized to the circular polynucleotide, wherein the splint oligonucleotide includes a probe sequence complement hybridized to the probe sequence of the circular polynucleotide, and wherein the splint oligonucleotide includes a target sequence hybridized to the target sequence complement of the circular polynucleotide. In embodiments, the splint oligonucleotide further includes a spacer sequence located between the probe sequence complement and the target sequence. In embodiments, the complex is inside of a cell. In embodiments, the complex is inside a tissue section. In embodiments, the cell or tissue is attached to a solid support. The solid supports for some embodiments have at least one surface located within a flow cell or reaction chamber. Flow cells provide a convenient format for housing an array of clusters produced by the methods described herein, in particular when subjected to sequencing (e.g., SBS) or other detection technique that involves repeated delivery of reagents in cycles.

[0122] In embodiments, the solid support includes a glass substrate. In embodiments, the glass substrate is a borosilicate glass substrate with a composition including SiCh, AI2O3, B2O3, Li2O, Na2O, K2O, MgO, CaO, SrO, BaO, ZnO, TiCh, ZrCh, P2O5, or a combination thereof (see e.g., US Patent No. 10,974,990). In embodiments, the glass substrate is an alkaline earth boro- aluminosilicate glass substrate. In embodiments, the solid support includes a channel bored into the solid support. In embodiments, the solid support includes a plurality of channels bored into the solid support. In embodiments, the solid support includes 2 channels bored into the solid support. In embodiments, the solid support includes 3channels bored into the solid support. In embodiments, the solid support includes 4 channels bored into the solid support. In embodiments, the width of the channel is from about 1 to 5 mm. In embodiments, the width of the channel is from about 5 to 10 mm. In embodiments, the width of the channel is from about 10 to 15 mm. In embodiments, the width of the channel is from about 5 mm. In embodiments, the width of the channel is from about 11 mm.

[0123] In embodiments, the solid support includes a gasket, wherein the gasket defines a reaction chamber wherein the cell or tissue is contained. In embodiments, the gasket includes silicone, polyimide, fluorocarbon elastomer, ethylene propylene diene, polychloroprene, polytetrafluoroethylene, nitrile rubber, butyl rubber, natural rubber, thermoplastic elastomer, or a combination thereof. In embodiments, the second solid support includes a spacer structure which forms a channel. The spacer structure may be made of any suitable material, for example resin, glass, plastic, silicon, an adhesive, or a combination thereof. In embodiments, the spacer includes a first adhesive in contact with a functionalized glass slide and second adhesive in contact with a second solid support.

[0124] In embodiments, the solid support includes a resist (e.g., a nanoimprint lithography (NIL) resist). Nanoimprint resists can include thermal curable materials (e.g., thermoplastic polymers), and/or UV-curable polymers. In embodiments, the solid support is generated by pressing a transparent mold possessing the pattern of interest (e.g., the pattern of wells) into photo-curable liquid film, followed by solidifying the liquid materials via a UV light irradiation. Typical UV-curable resists have low viscosity, low surface tension, and suitable adhesion to the glass substrate. For example, the solid support surface, but not the surface of the wells, is coated in an organically modified ceramic polymer (ORMOCER®, registered trademark of Fraunhofer- Gesellschaft zur Fbrderung der angewandten Forschung e. V. in Germany). Organically modified ceramics contain organic side chains attached to an inorganic siloxane backbone. Several ORMOCER® polymers are now provided under names such as “Ormocore”, “Ormoclad” and “Ormocomp” by Micro Resist Technology GmbH. In embodiments, the solid support includes a resist as described in Haas et al Volume 351, Issues 1-2, 30 August 1999, Pages 198-203, US 2015/0079351A1, US 2008/0000373, or US 2010/0160478, each of which is incorporated herein by reference. In embodiments, the solid support surface is coated in an organically modified ceramic polymer (ORMOCER®, registered trademark of Fraunhofer-Gesellschaft zur Forderung der angewandten Forschung e. V. in Germany).

[0125] In embodiments, the solid support includes a polymer layer. In embodiments, the polymer layer includes polymerized units of alkoxysilyl methacrylate, alkoxysilyl acrylate, alkoxysilyl methylacrylamide, alkoxysilyl methylacrylamide, or a copolymer thereof. In embodiments, the polymer layer includes polymerized units of alkoxysilyl methacrylate. In embodiments, the polymer layer includes polymerized units of alkoxysilyl acrylate. In embodiments, the polymer layer includes polymerized units of alkoxysilyl methylacrylamide. In embodiments, the polymer layer includes polymerized units of alkoxysilyl methylacrylamide. In embodiments, the polymer layer includes glycidyloxypropyl-trimethyloxysilane. In embodiments, the polymer layer includes methacryloxypropyl-trimethoxysilane. In embodiments, the polymer layer includes polymerized units of

In embodiments, the polymer layer is an organically-modified ceramic polymer. In embodiments, the polymer includes polymerized monomers of alkoxysilyl polymers, such as

the solid support includes polymerized units

embodiments, the solid support includes polymerized units

embodiments, the solid support includes polymerized unites of

embodiments, the polymer layer includes one or more ceramic particles, (e.g., silicates, aluminates, and titanates). In embodiments, the polymer layer includes titanium dioxide, zinc oxide, and/or iron oxide. [0126] In an aspect is provided a complex including: i) a circular polynucleotide including, from 5’ to 3’, a probe sequence, a target hybridization sequence, a subject sequence complement, and a target sequence complement; and ii) a splint oligonucleotide hybridized to the circular polynucleotide, wherein the splint oligonucleotide includes, from 5’ to 3’, a probe sequence complement hybridized to the probe sequence of the circular polynucleotide, and a target sequence hybridized to the target sequence complement of the circular polynucleotide. In embodiments, the splint oligonucleotide further includes a spacer sequence located between the probe sequence complement and the target sequence. In embodiments, the complex is inside of a cell. In embodiments, the complex is inside a tissue section.

[0127] In embodiments, the circular polynucleotide further includes a single-stranded sequence at a 3’ end. In embodiments, the single-stranded sequence includes between about 5 to about 100 nucleotides. In embodiments, the single-stranded sequence includes between about 25 to about 250 nucleotides. In embodiments, the single-stranded sequence includes between about 50 to about 500 nucleotides. In embodiments, the single-stranded sequence includes more than 500 nucleotides. In embodiments, the single-stranded sequence includes about 25, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, or 500 nucleotides.

[0128] In embodiments, the splint oligonucleotide further includes a spacer sequence (i.e., a spacer sequence as described herein) between the target sequence and the probe sequence complement. In embodiments, the spacer sequence includes a primer binding sequence. In embodiments, the spacer sequence includes a barcode sequence. In embodiments, the probe sequence of the circular polynucleotide includes one or more primer binding sequences. In embodiments, the circular polynucleotide includes a sequencing primer binding sequence.

[0129] In embodiments, the complex is in a cell. In embodiments, the cell is attached to a substrate. In embodiments, the cell is attached to the substrate via a bioconjugate reactive moiety. In embodiments, the cell is attached to a well of a microplate (e.g., a microplate including a plurality of wells, wherein one or more wells include a plurality of cells). In embodiments, each cell of the one or more wells includes the complex. In embodiments, each cell of the one or more wells includes a plurality of complexes. In embodiments, the complex in each well of the plurality of wells includes a different subject sequence. In embodiments, the complex in each cell of the plurality of wells includes the same subject sequence. In embodiments, the cells in each well include a plurality of different complexes (e.g., the plurality of cells in the well include one or more complexes including different subject sequences, or complements thereof). In embodiments, the complex is within a cell or tissue sample. In embodiments, the cell including the complex is within a tissue section. In embodiments, the cell or tissue sample is cleared (e.g., digested) of proteins, lipids, or proteins and lipids. In embodiments, the cell or tissue sample is processed according to a known technique in the art, for example CLARITY (Chung K., et al. Nature 497, 332-337 (2013)), PACT-PARS (Yang Bet al. Cell 158, 945-958 (2014).), CUBIC (Susaki E. A. et al. Cell 157, 726-739 (2014)., 18), ScaleS (Hama H., et al. Nat. Neurosci. 18, 1518-1529 (2015)), OPTIClear (Lai H. M., et al. Nat. Commun. 9, 1066 (2018)), Ce3D (Li W., et al. Proc. Natl. Acad. Sci. U.S.A. 114, E7321-E7330 (2017)), BABB (Dodt H.U. et al. Nat. Methods 4, 331-336 (2007)), iDISCO (Renier N., et al. Cell 159, 896-910 (2014)), uDISCO (Pan C., et al. Nat. Methods 13, 859-867 (2016)), FluoClearBABB (Schwarz M. K., et al. PLOS ONE 10, e0124650 (2015)), Ethanol-ECi (Klingberg A., et al. J. Am. Soc. Nephrol. 28, 452-459 (2017)), and PEGASOS (Jing D. et al. Cell Res. 28, 803-818 (2018)).

[0130] In an aspect, provided herein are kits for use in accordance with any of the compounds, compositions, or methods disclosed herein, and including one or more elements thereof. In embodiments, a kit includes labeled nucleotides including differently labeled nucleotides, enzymes, buffers, oligonucleotides, and related solvents and solutions. In embodiments, the kit includes one or more oligonucleotide probes (e.g., an oligonucleotide probe as described herein). The kit may also include a template nucleic acid (DNA and/or RNA), one or more primer polynucleotides, nucleoside triphosphates (including, e.g., deoxyribonucleotides, dideoxynucleotides, ribonucleotides, labeled nucleotides, and/or modified nucleotides), buffers, salts, and/or labels (e.g., fluorophores). In embodiments, the kit includes components useful for circularizing template polynucleotides using a ligation enzyme (e.g., Circligase enzyme, Taq DNA Ligase, HiFi Taq DNA Ligase, T4 ligase, SplintR® ligase, or Ampligase DNA Ligase). For example, such a kit further includes the following components: (a) reaction buffer for controlling pH and providing an optimized salt composition for a ligation enzyme (e.g., Circligase enzyme, Taq DNA Ligase, HiFi Taq DNA Ligase, T4 ligase, SplintR ligase, or Ampligase DNA Ligase), and (b) ligation enzyme cofactors. In embodiments, the kit further includes instructions for use thereof. In embodiments, kits described herein include a polymerase. In embodiments, the polymerase is a DNA polymerase. In embodiments, the DNA polymerase is a thermophilic nucleic acid polymerase. In embodiments, the DNA polymerase is a modified archaeal DNA polymerase. In embodiments, the kit includes a sequencing solution. In embodiments, the sequencing solution include labeled nucleotides including differently labeled nucleotides, wherein the label (or lack thereof) identifies the type of nucleotide. For example, each adenine nucleotide, or analog thereof; a thymine nucleotide; a cytosine nucleotide, or analog thereof; and a guanine nucleotide, or analog thereof may be labeled with a different fluorescent label. [0131] In an aspect is provided a kit including: a) an oligonucleotide probe including a target hybridization sequence and a probe sequence, wherein the target hybridization sequence is complementary to a probe hybridization sequence in a target polynucleotide; and b) a splint oligonucleotide including a target sequence and a probe sequence complement, wherein the target sequence is substantially identical to a sequence in the target polynucleotide, and wherein the probe sequence complement is capable of hybridizing to the probe sequence of the oligonucleotide probe. In embodiments, the splint oligonucleotide further includes a spacer sequence.

[0132] In an aspect is provided a kit including a plurality of oligonucleotide probes (e.g., oligonucleotide probes as described herein) and a plurality of splint oligonucleotides (e.g., splint oligonucleotides as described herein). In embodiments, each of the plurality of oligonucleotide probes include a target hybridization sequence capable of hybridizing to a sequence of a target polynucleotide (e.g., is complementary to a probe hybridization sequence in a target polynucleotide) and a probe sequence. In embodiments, the probe sequence is the same sequence in each oligonucleotide probe of the plurality. In embodiments, the probe sequence is a different sequence in each oligonucleotide probe of the plurality. In embodiments, the probe sequence includes one or more primer binding sequences (e.g., one or more amplification primer binding sequences). In embodiments, each target hybridization sequence of the plurality of oligonucleotide probes is complementary to a different sequence of the target polynucleotide (e.g., is complementary to a different probe hybridization sequence in a target polynucleotide). In embodiments, each target hybridization sequence of the plurality of oligonucleotide probes is complementary to a different sequence of a different target polynucleotide (e.g., is complementary to a different probe hybridization sequence in different target polynucleotides). In embodiments, each target hybridization sequence of the plurality of oligonucleotide probes is complementary to a different sequence of the same target polynucleotide (e.g., is complementary to a different probe hybridization sequence in the same target polynucleotide).

[0133] In embodiments, the target hybridization sequence of the oligonucleotide probe is greater than 30 nucleotides. In embodiments, the target hybridization sequence of the oligonucleotide probe is about 5 to about 35 nucleotides in length. In embodiments, the target hybridization sequence is about 12 to 15 nucleotides in length. In embodiments, the target hybridization sequence is about 35 to 40 nucleotides in length to maximize specificity. In embodiments, the target hybridization sequence is greater than 12 nucleotides in length. In embodiments, the target hybridization sequence is about 5, about 10, about 15, about 20, about 25, about 30, or about 35 nucleotides in length. In embodiments, the target hybridization sequence of each oligonucleotide primer is a single stranded polynucleotide that is at least 50% complementary, at least 75% complementary, at least 85% complementary, at least 90% complementary, at least 95% complementary, at least 98%, at least 99% complementary, or 100% complementary to a portion of a target polynucleotide.

[0134] In embodiments, the target hybridization sequence of each oligonucleotide probe (e.g., each oligonucleotide probe of a plurality of oligonucleotide probe) is complementary to different portions of the same target polynucleotide. In embodiments, the target hybridization sequence of each oligonucleotide probe (e.g., each oligonucleotide probe of a plurality of oligonucleotide probes) is complementary to different portions of different target polynucleotides. In embodiments, the target hybridization sequence of each oligonucleotide probe is complementary to portions of the same target polynucleotide that are separated by about 10 to about 500 nucleotides. In embodiments, the target hybridization sequence of each oligonucleotide probe are complementary to portions of the same target polynucleotide that are separated by about 10, about 15, about 20, about 25, about 30, about 35, about 40, about 45, about 50, about 75, about 100, about 125, about 150, about 175, about 200, about 225, about 250, about 275, about 300, about 325, about 350, about 375, about 400, about 425, about 450, about 475, or about 500 nucleotides. In embodiments, the target hybridization sequence of each oligonucleotide probe is complementary to portions of the same target polynucleotide that are separated by about or more than about 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, or 500 nucleotides.

[0135] In embodiments, the probe sequence of the oligonucleotide probe is greater than 30 nucleotides. In embodiments, the probe sequence of each oligonucleotide probe is about 5 to about 35 nucleotides in length. In embodiments, the probe sequence is about 12 to 15 nucleotides in length. In embodiments, the probe sequence is about 35 to 40 nucleotides in length. In embodiments, the probe sequence is about 40 to 50 nucleotides in length. In embodiments, the probe sequence is greater than 50 nucleotides in length. In embodiments, the probe sequence is about 5, about 10, about 15, about 20, about 25, about 30, about 35, about 40, about 45, or about 50 nucleotides in length.

[0136] In embodiments, each oligonucleotide probe (e.g., each oligonucleotide probe of a plurality of oligonucleotide probes) includes a primer binding sequence (i.e., a sequence complementary to a primer, such as an amplification or sequencing primer). In embodiments, the splint oligonucleotide includes a primer binding sequence. [0137] In embodiments, each oligonucleotide probe includes about 50 to about 150 nucleotides. In embodiments, the splint oligonucleotide includes about 30 to about 150 nucleotides. In embodiments, each oligonucleotide probe includes about 50 to about 300 nucleotides. In embodiments, the splint oligonucleotide includes about 30 to about 300 nucleotides. In embodiments, the splint oligonucleotide includes about 50 to about 300 nucleotides. In embodiments, each oligonucleotide probe includes about or more than about 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, or 500 nucleotides. In embodiments, the splint oligonucleotide includes about or more than about 30, 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, or 500 nucleotides. In embodiments, each oligonucleotide probe includes less than about 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, or 500 nucleotides. In embodiments, the splint oligonucleotide includes less than about 30, 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, or 500 nucleotides.

[0138] In embodiments, each oligonucleotide probe includes about 50 to about 150 nucleotides. In embodiments, each oligonucleotide probe includes about 50 to about 300 nucleotides. In embodiments, each oligonucleotide probe includes about 50 to about 500 nucleotides. In embodiments, each oligonucleotide probe includes about or more than about 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, or 500 nucleotides. In embodiments, each oligonucleotide probe includes less than 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, or 500 nucleotides.

[0139] In embodiments, the splint oligonucleotide includes about 30 to about 150 nucleotides. In embodiments, the splint oligonucleotide includes about 30 to about 300 nucleotides. In embodiments, the splint oligonucleotide includes about 30 to about 500 nucleotides. In embodiments, the splint oligonucleotide includes about or more than about 30, 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, or 500 nucleotides. In embodiments, the splint oligonucleotide includes less than 30, 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, or 500 nucleotides.

[0140] In embodiments, the splint oligonucleotide includes a target sequence (e.g., a sequence that is the same, or substantially the same, as a sequence of the target polynucleotide). In embodiments, the target sequence includes about 5 to about 50 nucleotides. In embodiments, the target sequence includes about 15 to about 40 nucleotides. In embodiments, the target sequence includes about 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50 nucleotides.

[0141] In embodiments, the splint oligonucleotide includes a spacer sequence (e.g., a sequence located between the probe sequence complement and the target sequence). In embodiments, the spacer sequence includes about 5 to about 20 nucleotides. In embodiments, the spacer sequence includes about 5, 10, 15, or 20 nucleotides. In embodiments, each nucleotide of the spacer sequence is the same (e.g., all the nucleotides of the spacer sequence consist of adenine, thymine, cytosine, or guanine).

[0142] In embodiments, each oligonucleotide probe and/or splint oligonucleotide include a barcode sequence. In embodiments, the barcode (i.e., the barcode sequence) is at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 nucleotides in length. In embodiments, the barcode is 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 nucleotides in length. In embodiments, the barcode is 10 to 15 nucleotides in length. In embodiments, the barcode is at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or more nucleotides in length. In embodiments, the barcode can be at most about 300, 200, 100, 90, 80, 70, 60, 50, 40, 30, 20, 15, 12, 10, 9, 8, 7, 6, 5, 4 or fewer or more nucleotides in length. In embodiments, the barcode includes between about 5 to about 8, about 5 to about 10, about 5 to about 15, about 5 to about 20, about 10 to about 150 nucleotides. In embodiments, the barcode includes between 5 to 8, 5 to 10, 5 to 15, 5 to 20, 10 to 150 nucleotides. In embodiments, the barcode is 10 nucleotides. In embodiments, the barcode may include a unique sequence (e.g., a barcode sequence) that gives the barcode its identifying functionality. The unique sequence may be random or non-random. In embodiments, the barcode is known (i.e., the nucleic sequence is known before sequencing) and is sorted into a basis-set according to their Hamming distance. Oligonucleotide barcodes (e.g., barcode sequences included in an oligonucleotide) can be associated with a target of interest by knowing, a priori, the target of interest, such as a gene or protein. In embodiments, the barcodes further include one or more sequences capable of specifically binding a gene or nucleic acid sequence of interest. For example, in embodiments, the barcode includes a sequence capable of hybridizing to mRNA, e.g., one containing a poly-T sequence (e.g., having several T's in a row, e.g., 4, 5, 6, 7, 8, or more T's).

[0143] In embodiments, the barcode is included as part of an oligonucleotide of longer sequence length, such as a primer or a random sequence (e.g., a random N-mer). In embodiments, the barcode contains random sequences to increase the mass or size of the oligonucleotide tag. The random sequence can be of any suitable length, and there may be one or more than one present. As non-limiting examples, the random sequence may have a length of 10 to 40, 10 to 30, 10 to 20, 25 to 50, 15 to 40, 15 to 30, 20 to 50, 20 to 40, or 20 to 30 nucleotides. In embodiments, each barcode sequence is selected from a known set of barcode sequences. In embodiments, each of the known set of barcode sequences is associated with a target hybridization sequence from a known set of target hybridization sequences. In embodiments, a first barcode sequence is associated with a first target hybridization sequence, and wherein a second barcode sequence is associated with a second target hybridization sequence (e.g., wherein the second target hybridization sequence is included in an oligonucleotide targeting a different target nucleic acid than the first target hybridization sequence). In embodiments, the same barcode sequence is associated with a plurality of oligonucleotides targeting different sequences of the same target nucleic acid (e.g., the same target polynucleotide).

[0144] In embodiments, the target nucleic acid (i.e., the target polynucleotide) includes a nucleic acid sequence encoding a TCR alpha chain, a TCR beta chain, a TCR delta chain, a TCR gamma chain, or any fragment thereof (e.g., variable regions including VDJ or VJ regions, constant regions, transmembrane regions, fragments thereof, combinations thereof, and combinations of fragments thereof). In embodiments, the target nucleic acid includes a nucleic acid sequence encoding a B cell receptor heavy chain, B cell receptor light chain, or any fragment thereof (e.g., variable regions including VDJ or VJ regions, constant regions, transmembrane regions, fragments thereof, combinations thereof, and combinations of fragments thereof). In embodiments, the target nucleic acid includes a CDR3 nucleic acid sequence. In embodiments, the target nucleic acid includes a TCRA gene sequence or a TCRB gene sequence. In embodiments, the target nucleic acid includes a TCRA gene sequence and a TCRB gene sequence. In embodiments, the target nucleic acid includes sequences of various T cell receptor alpha variable genes (TRAV genes), T cell receptor alpha joining genes (TRAJ genes), T cell receptor alpha constant genes (TRAC genes), T cell receptor beta variable genes (TRBV genes), T cell receptor beta diversity genes (TRBD genes), T cell receptor beta joining genes (TRB J genes), T cell receptor beta constant genes (TRBC genes), T cell receptor gamma variable genes (TRGV genes), T cell receptor gamma joining genes (TRGJ genes), T cell receptor gamma constant genes (TRGC genes), T cell receptor delta variable genes (TRDV genes), T cell receptor delta diversity genes (TRDD genes), T cell receptor delta joining genes (TRDJ genes), or T cell receptor delta constant genes (TRDC genes).

[0145] In embodiments, the target polynucleotide includes a cancer-associated gene nucleic acid sequence, a viral nucleic acid sequence, a bacterial nucleic acid sequence, or a fungal nucleic acid sequence. In embodiments, the cancer-associated gene is a nucleic acid sequence identified within The Cancer Genome Atlas Program, accessible at www.cancer.gov/tcga.

[0146] In embodiments, the target polynucleotide includes a CD4, CD68, CD20, CD11c, CD8, HLA-DR, Ki67, CD45RO, PanCK, CD3e, CD44, CD45, HLA-A, CD14, CD56, CD57, CD19, CD2, CDla, CD107a, CD21, Pax5, FOXP3, Granzyme B, CD38, CD39, CD79a, TIGIT, TOX, TP63, S100A4, TFAM, GP100, LaminBl, CK19, CK17, GAT A3, SOX2, Bcl2, EpCAM, Caveolin, CD163, CDl lb, MPO, CD141, iNOS, PD-1, PD-L1, ICOS, TIM3, LAG3, IDO1, CD40, HLA-E, IFNG, CD69, E-cadherin, CD31, Histone H3, Beta-actin, Podoplanin, SMA, Vimentin, Collagen IV, CD34, Beta-catenin, MMP-9, ZEB1, ASCT2, Na/K ATPase, HK1, LDHA, G6PD, IDH2, GLUT1, pNRF2, ATPA5, SDHA, Citrate Synthase, CPT1A, PARP, BAK, BCL-XL, BAX, BAD, Cytochrome c, LC3B, Beclin-1, H2AX, pRPS6, PCNA, Cyclin DI, HLA- DPB1, LEF1, GAL9, CD 138, MC Tryptase, 0X40, ZAP70, CD7, ClQa, CCR6, CD 15, AXL, and/or CD227 nucleic acid sequence.

[0147] In embodiments, the target polynucleotide can include any polynucleotide of interest. The polynucleotide can include DNA, RNA, peptide nucleic acid, morpholino nucleic acid, locked nucleic acid, glycol nucleic acid, threose nucleic acid, mixtures thereof, and hybrids thereof. In embodiments, the polynucleotide is obtained from one or more source organisms. In some embodiments, the polynucleotide can include a selected sequence or a portion of a larger sequence. In embodiments, sequencing a portion of a polynucleotide or a fragment thereof can be used to identify the source of the polynucleotide. With reference to nucleic acids, polynucleotides and/or nucleotide sequences a “portion,” “fragment” or “region” can be at least 5 consecutive nucleotides, at least 10 consecutive nucleotides, at least 15 consecutive nucleotides, at least 20 consecutive nucleotides, at least 25 consecutive nucleotides, at least 50 consecutive nucleotides, at least 100 consecutive nucleotides, or at least 150 consecutive nucleotides.

[0148] In embodiments, the entire sequence of the target polynucleotide is about 1 to 3kb, and only a portion of that target (e.g., 50 to 100 nucleotides) is sequenced. In embodiments, the target polynucleotide is about 1 to 3kb. In embodiments, the target polynucleotide is about 1 to 2kb. In embodiments, the target polynucleotide is about Ikb. In embodiments, the target polynucleotide is about 2kb. In embodiments, the target polynucleotide is less than Ikb. In embodiments, the target polynucleotide is about 500 nucleotides. In embodiments, the target polynucleotide is about 200 nucleotides. In embodiments, the target polynucleotide is about 100 nucleotides. In embodiments, the target polynucleotide is less than 100 nucleotides. In embodiments, the target polynucleotide is about 5 to 50 nucleotides.

[0149] In embodiments, the target polynucleotide is an RNA nucleic acid sequence or DNA nucleic acid sequence. In embodiments, the target polynucleotide is an RNA nucleic acid sequence or DNA nucleic acid sequence from the same cell. In embodiments, the target polynucleotide is an RNA nucleic acid sequence. In embodiments, the RNA nucleic acid sequence is stabilized using known techniques in the art. For example, RNA degradation by RNase should be minimized using commercially available solutions, e.g., RNA Later®, RNA Lysis Buffer, or Keratinocyte serum-free medium). In embodiments, the target polynucleotide is messenger RNA (mRNA), transfer RNA (tRNA), micro RNA (miRNA), small interfering RNA (siRNA), small nucleolar RNA (snoRNA), small nuclear RNA (snRNA), Piwi-interacting RNA (piRNA), enhancer RNA (eRNA), or ribosomal RNA (rRNA). In embodiments, the target polynucleotide is pre-mRNA. In embodiments, the target polynucleotide is heterogeneous nuclear RNA (hnRNA). In embodiments, the target polynucleotide is mRNA, tRNA (transfer RNA), rRNA (ribosomal RNA), or noncoding RNA (such as IncRNA (long noncoding RNA)). In embodiments, the target polynucleotides are on different regions of the same RNA nucleic acid sequence.

[0150] In embodiments, the target polynucleotide includes RNA nucleic acid sequences. In embodiments the target polynucleotide is an RNA transcript. In embodiments the target polynucleotide is a single stranded RNA nucleic acid sequence. In embodiments, the target polynucleotide is an RNA nucleic acid sequence or a DNA nucleic acid sequence (e.g., cDNA). In embodiments, the target polynucleotide is a cDNA target polynucleotide nucleic acid sequence and before step a), the RNA nucleic acid sequence is reverse transcribed to generate the cDNA target polynucleotide nucleic acid sequence. In embodiments, reverse transcription of the RNA nucleic acid is performed with a reverse transcriptase, for example, Tth DNA polymerase or mutants thereof. In embodiments, the target polynucleotide is genomic DNA (gDNA), mitochondrial DNA, chloroplast DNA, episomal DNA, viral DNA, or copy DNA (cDNA). In embodiments, the target polynucleotide is coding RNA such as messenger RNA (mRNA), and non-coding RNA (ncRNA) such as transfer RNA (tRNA), microRNA (miRNA), small nuclear RNA (snRNA), or ribosomal RNA (rRNA). In embodiments, the target polynucleotide is a cancer-associated gene. In embodiments, to minimize amplification errors or bias, the target polynucleotide is not reverse transcribed to generate cDNA.

[0151] In embodiments, each oligonucleotide probe (e.g., one or more oligonucleotide probes of a plurality of oligonucleotide probes) includes locked nucleic acids (LNAs), Bis-locked nucleic acids (bisLNAs), twisted intercalating nucleic acids (TINAs), bridged nucleic acids (BNAs), 2’- O-methyl RNA:DNA chimeric nucleic acids, minor groove binder (MGB) nucleic acids, morpholino nucleic acids, C5-modified pyrimidine nucleic acids, peptide nucleic acids (PNAs), or combinations thereof. In embodiments, the circularizable oligonucleotide includes locked nucleic acids (LNAs), Bis-locked nucleic acids (bisLNAs), twisted intercalating nucleic acids (TINAs), bridged nucleic acids (BNAs), 2’-O-methyl RNA:DNA chimeric nucleic acids, minor groove binder (MGB) nucleic acids, morpholino nucleic acids, C5-modified pyrimidine nucleic acids, peptide nucleic acids (PNAs), or combinations thereof.

[0152] In embodiments, each splint oligonucleotide (e.g., one or more splint oligonucleotides of a plurality of splint oligonucleotides) includes locked nucleic acids (LNAs), Bis-locked nucleic acids (bisLNAs), twisted intercalating nucleic acids (TINAs), bridged nucleic acids (BNAs), 2’- O-methyl RNA:DNA chimeric nucleic acids, minor groove binder (MGB) nucleic acids, morpholino nucleic acids, C5-modified pyrimidine nucleic acids, peptide nucleic acids (PNAs), or combinations thereof. In embodiments, the circularizable oligonucleotide includes locked nucleic acids (LNAs), Bis-locked nucleic acids (bisLNAs), twisted intercalating nucleic acids (TINAs), bridged nucleic acids (BNAs), 2’-O-methyl RNA:DNA chimeric nucleic acids, minor groove binder (MGB) nucleic acids, morpholino nucleic acids, C5-modified pyrimidine nucleic acids, peptide nucleic acids (PNAs), or combinations thereof.

[0153] In embodiments, each oligonucleotide probe includes one or more locked nucleic acid (LNA) nucleotides. In embodiments, the target hybridization sequence of each oligonucleotide probe includes one or more LNA nucleotides. In embodiments, the probe sequence of each oligonucleotide probe includes one or more LNA nucleotides. In embodiments, the sequence complementary to the probe sequence of the splint oligonucleotide (e.g., the probe sequence complement) includes one or more LNA nucleotides.

[0154] In embodiments, the target hybridization sequence of the oligonucleotide probe includes a plurality of LNAs interspersed throughout the target hybridization sequence. In embodiments, the probe sequence (or complement thereof) of the oligonucleotide probe and/or splint oligonucleotide includes a plurality of LNAs interspersed throughout the probe sequence, or complement thereof.

[0155] In embodiments, the target hybridization sequence and/or probe sequence includes Bislocked nucleic acids (bisLNAs). In embodiments, the target hybridization sequence and/or probe sequence includes twisted intercalating nucleic acids (TINAs). In embodiments, the target hybridization sequence and/or probe sequence includes bridged nucleic acids (BNAs). In embodiments, the target hybridization sequence and/or probe sequence includes 2’-O-methyl RNA:DNA chimeric nucleic acids. In embodiments, the target hybridization sequence and/or probe sequence includes minor groove binder (MGB) nucleic acids. In embodiments, the target hybridization sequence and/or probe sequence includes morpholino nucleic acids. Morpholino nucleic acids are synthetic nucleotides that have standard nucleic acid bases (e.g., adenine, guanine, cytosine, and thymine) wherein those bases are bound to methylenemorpholine rings linked through phosphorodiamidate groups instead of phosphates. Morpholino nucleic acids may be referred to as phosphorodiamidate morpholino oligomers (PMOs). In embodiments, the target hybridization sequence and/or probe sequence includes C5-modified pyrimidine nucleic acids. In embodiments, the target hybridization sequence and/or probe sequence includes peptide nucleic acids (PNAs). In embodiments, the target hybridization sequence and/or probe sequence includes from 5' to 3' a plurality of synthetic nucleotides (e.g., LNAs) followed by a plurality (e.g., 2 to 5) canonical or native nucleotides (e.g., dNTPs). In embodiments, the target hybridization sequence and/or probe sequence includes one or more (e.g., 2 to 5) deoxyuracil nucleobases (dU). In embodiments, the one or more dU nucleobases are at or near the 3’ end of the target hybridization sequence and/or probe sequence (e.g., within 5 nucleotides of the 3’ end). In embodiments, the target hybridization sequence and/or probe sequence includes from 5' to 3' a plurality (e.g., 2 to 5) of phosphorothioate nucleic acids, followed by a plurality of synthetic nucleotides (e.g., LNAs), and subsequently followed by a plurality (e.g., 2 to 5) of canonical nucleobases. In some embodiments, the target hybridization sequence and/or probe sequence includes a plurality of canonical nucleobases, wherein the canonical nucleobases terminate (i.e., at the 3' end) with a deoxyuracil nucleobase (dU).

[0156] In embodiments, the target hybridization sequence and/or probe sequence includes a plurality of LNAs interspersed throughout the polynucleotide. In embodiments, the target hybridization sequence and/or probe sequence includes a plurality of consecutive LNAs (e.g., 2 to 5 LNAs, 5 to 7 LNAs, or 7 to 10 LNAs) throughout the target hybridization sequence and/or probe sequence. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes less than 70%, less than 60%, less than 50%, less than 40%, less than 30%, less than 20%, less than 10%, or less than 5% of LNAs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes up to about 70%, up to about 60%, up to about 50%, up to about 40%, up to about 30%, up to about 20%, up to about 10%, or up to about 5% of LNAs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes more than 60%, more than 50%, more than 40%, more than 30%, more than 20%, more than 10%, or more than 5% of LNAs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 5% to about 10%, about 10% to about 20%, about 20% to about 30%, about 30% to about 40%, about 40% to about 50%, about 50% to about 60%, or about 60% to about 70% of LNAs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 5%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, or about 70% of LNAs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, or about 95% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes less than 95%, less than 90%, less than 80%, less than 70%, less than 60%, less than 50%, less than 40%, or less than 30% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes up to about 95%, up to about 90%, up to about 80%, up to about 70%, up to about 60%, up to about 50%, up to about 40%, or up to about 30% of canonical dNTPs. In embodiments, the entire composition of the the target hybridization sequence and/or probe sequence includes more than 90%, more than 80%, more than 70%, more than 60%, more than 50%, more than 40%, or more than 30% of canonical dNTPs.

[0157] In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 70% of LNAs and about 30% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 65% of LNAs and about 35% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 60% of LNAs and about 40% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 55% of LNAs and about 45% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 50% of LNAs and about 50% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 45% of LNAs and about 55% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 40% of LNAs and about 60% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 35% of LNAs and about 65% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 30% of LNAs and about 70% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 25% of LNAs and about 75% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 20% of LNAs and about 80% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 15% of LNAs and about 85% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 10% of LNAs and about 90% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 5% of LNAs and about 95% of canonical dNTPs. [0158] In embodiments, each oligonucleotide includes a blocking moiety at a 3’ end (e.g., at the 3’ end of each oligonucleotide of a plurality of oligonucleotides). In embodiments, the blocking moiety is reversible. In embodiments, the blocking moiety is irreversible. In embodiments, the blocking moiety at the 3’ end (e.g., the 3’ blocking moiety) includes a reversible terminator. In embodiments, the 3’ blocking moiety includes a dideoxynucleotide triphosphate (e.g., a ddNTP).

[0159] In embodiments, the kit includes a microplate, and reagents for sample preparation and purification, amplification, and/or sequencing (e.g., one or more sequencing reaction mixtures). In embodiments, the kit includes for protein detection includes a plurality of specific binding agents linked to an oligonucleotide (e.g., DNA-conjugated antibodies).

[0160] In embodiments, the kit includes components useful for circularizing template polynucleotides using a ligation enzyme (e.g., Circligase enzyme, Taq DNA Ligase, HiFi Taq DNA Ligase, T4 ligase, SplintR ligase, or Ampligase DNA Ligase). For example, such a kit further includes the following components: (a) reaction buffer for controlling pH and providing an optimized salt composition for a ligation enzyme (e.g., Circligase enzyme, Taq DNA Ligase, HiFi Taq DNA Ligase, T4 ligase, SplintR ligase, or Ampligase DNA Ligase), and (b) ligation enzyme cofactors. In embodiments, the kit further includes instructions for use thereof. In embodiments, kits described herein include a polymerase. In embodiments, the polymerase is a DNA polymerase. In embodiments, the DNA polymerase is a thermophilic nucleic acid polymerase. In embodiments, the DNA polymerase is a modified archaeal DNA polymerase. In embodiments, the kit includes a sequencing solution. In embodiments, the sequencing solution include labeled nucleotides including differently labeled nucleotides, wherein the label (or lack thereof) identifies the type of nucleotide. For example, each adenine nucleotide, or analog thereof; a thymine nucleotide; a cytosine nucleotide, or analog thereof; and a guanine nucleotide, or analog thereof may be labeled with a different fluorescent label. In embodiments, the kit includes a modified terminal deoxynucleotidyl transferase (TdT) enzyme.

[0161] In embodiments, the kit further includes a ligase. In embodiments, the kit includes one or more ligases. In embodiments, the kit includes a plurality of ligases. In embodiments, the kit further includes a polymerase. In embodiments, the kit further includes one or more polymerases. In embodiments, the kit includes a plurality of polymerases. In embodiments, the kit includes a ligase and one or more polymerases. In embodiments, the one or more polymerases include a reverse transcriptase. Exemplary reverse transcriptases include, but are not limited to, HIV-1 reverse transcriptase from human immunodeficiency virus type 1 (PDB 1HMV), HIV-2 reverse transcriptase from human immunodeficiency virus type 2, M-MLV reverse transcriptase from the Moloney murine leukemia virus, AMV reverse transcriptase from the avian myeloblastosis virus, and Telomerase reverse transcriptase. In embodiments, the polymerase is a Thermus thermophilus (Tth) DNA polymerase or mutant thereof. In embodiments, the polymerase is a Reverse Transcription Xenopolymerase (RTX). In embodiments, the polymerase is a mutant M-MLV reverse transcriptase from the Moloney murine leukemia virus.

[0162] In embodiments, the kit further includes an exonuclease, wherein the exonuclease is capable of removing a single-stranded nucleic acid sequence. In embodiments, the exonuclease is Exonuclease I. In embodiments, the exonuclease is Exonuclease T. In embodiments, the kit further includes an exonuclease-compatible buffer (e.g., a buffer wherein the exonuclease retains catalytic activity).

[0163] In embodiments, the kit includes a sequencing polymerase, and one or more amplification polymerases. In embodiments, the sequencing polymerase is capable of incorporating modified nucleotides. In embodiments, the polymerase is a DNA polymerase. In embodiments, the DNA polymerase is a Pol I DNA polymerase, Pol II DNA polymerase, Pol III DNA polymerase, Pol IV DNA polymerase, Pol V DNA polymerase, Pol P DNA polymerase, Pol p DNA polymerase, Pol X DNA polymerase, Pol c DNA polymerase, Pol a DNA polymerase, Pol 5 DNA polymerase, Pol a DNA polymerase, Pol q DNA polymerase, Pol r DNA polymerase, Pol K DNA polymerase, Pol C, DNA polymerase, Pol y DNA polymerase, Pol 9 DNA polymerase, Pol u DNA polymerase, or a thermophilic nucleic acid polymerase (e.g., Therminator y, 9°N polymerase (exo-), Therminator II, Therminator III, or Therminator IX). In embodiments, the DNA polymerase is a thermophilic nucleic acid polymerase. In embodiments, the DNA polymerase is a modified archaeal DNA polymerase. In embodiments, the polymerase is a reverse transcriptase. In embodiments, the polymerase is a mutant P. abyssi polymerase (e.g., such as a mutant P. abyssi polymerase described in WO 2018/148723 or WO 2020/056044, each of which are incorporated herein by reference for all purposes). In embodiments, the kit includes a stranddisplacing polymerase. In embodiments, the kit includes a strand-displacing polymerase, such as a phi29 polymerase, phi29 mutant polymerase or a thermostable phi29 mutant polymerase.

[0164] In embodiments, the kit includes a buffered solution. Typically, the buffered solutions contemplated herein are made from a weak acid and its conjugate base or a weak base and its conjugate acid. For example, sodium acetate and acetic acid are buffer agents that can be used to form an acetate buffer. Other examples of buffer agents that can be used to make buffered solutions include, but are not limited to, Tris, bicine, tricine, HEPES, TES, MOPS, MOPSO and PIPES. Additionally, other buffer agents that can be used in enzyme reactions, hybridization reactions, and detection reactions are known in the art. In embodiments, the buffered solution can include Tris. With respect to the embodiments described herein, the pH of the buffered solution can be modulated to permit any of the described reactions. In some embodiments, the buffered solution can have a pH greater than pH 7.0, greater than pH 7.5, greater than pH 8.0, greater than pH 8.5, greater than pH 9.0, greater than pH 9.5, greater than pH 10, greater than pH 10.5, greater than pH 11.0, or greater than pH 11.5. In other embodiments, the buffered solution can have a pH ranging, for example, from about pH 6 to about pH 9, from about pH 8 to about pH 10, or from about pH 7 to about pH 9. In embodiments, the buffered solution can include one or more divalent cations. Examples of divalent cations can include, but are not limited to, Mg2+, Mn2+, Zn2+, and Ca2+. In embodiments, the buffered solution can contain one or more divalent cations at a concentration sufficient to permit hybridization of a nucleic acid. In embodiments, the buffered solution can contain one or more divalent cations at a concentration sufficient to permit hybridization of a nucleic acid. In embodiments, the buffered solution includes about 10 mM Tris, about 20 mM Tris, about 30 mM Tris, about 40 mM Tris, or about 50 mM Tris. In embodiments the buffered solution includes about 50 mM NaCl, about 75 mM NaCl, about 100 mM NaCl, about 125 mM NaCl, about 150 mM NaCl, about 200 mM NaCl, about 300 mM NaCl, about 400 mM NaCl, or about 500 mM NaCl. In embodiments, the buffered solution includes about 0.05 mM EDTA, about 0.1 mM EDTA, about 0.25 mM EDTA, about 0.5 mM EDTA, about 1.0 mM EDTA, about 1.5 mM EDTA or about 2.0 mM EDTA. In embodiments, the buffered solution includes about 0.01% Triton X-100, about 0.025% Triton X-100, about 0.05% Triton X-100, about 0.1% Triton X-100, or about 0.5% Triton X-100. In embodiments, the buffered solution includes 20 mM Tris pH 8.0, 100 mM NaCl, 0.1 mM EDTA, 0.025% Triton X-100. In embodiments, the buffered solution includes 20 mM Tris pH 8.0, 150 mM NaCl, 0.1 mM EDTA, 0.025% Triton X-100. In embodiments, the buffered solution includes 20 mM Tris pH 8.0, 300 mM NaCl, 0.1 mM EDTA, 0.025% Triton X-100. In embodiments, the buffered solution includes 20 mM Tris pH 8.0, 400 mM NaCl, 0.1 mM EDTA, 0.025% Triton X-100. In embodiments, the buffered solution includes 20 mM Tris pH 8.0, 500 mM NaCl, 0.1 mM EDTA, 0.025% Triton X- 100.

[0165] In embodiments, the kit includes one or more sequencing reaction mixtures. In embodiments, the sequencing reaction mixture includes a buffer. In embodiments, the buffer includes an acetate buffer, 3-(N-morpholino)propanesulfonic acid (MOPS) buffer, N-(2- Acetamido)-2-aminoethanesulfonic acid (ACES) buffer, phosphate-buffered saline (PBS) buffer, 4-(2 -hydroxy ethyl)- 1 -piperazineethanesulfonic acid (HEPES) buffer, N-(l,l-Dimethyl-2- hydroxyethyl)-3-amino-2-hydroxypropanesulfonic acid (AMPSO) buffer, borate buffer (e.g., borate buffered saline, sodium borate buffer, boric acid buffer), 2-Amino-2-methyl-l,3- propanediol (AMPD) buffer, N-cy cl ohexyl-2-hydroxyl-3 -aminopropanesulfonic acid (CAPSO) buffer, 2-Amino-2-methyl-l -propanol (AMP) buffer, 4-(Cyclohexylamino)-l -butanesulfonic acid (CABS) buffer, glycine-NaOH buffer, N-Cyclohexyl-2-aminoethanesulfonic acid (CHES) buffer, tri s(hydroxymethyl)aminom ethane (Tris) buffer, or a N-cy cl ohexyl-3 -aminopropanesulfonic acid (CAPS) buffer. In embodiments, the buffer is a borate buffer. In embodiments, the buffer is a CHES buffer. In embodiments, the sequencing reaction mixture includes nucleotides, wherein the nucleotides include a reversible terminating moiety and a label covalently linked to the nucleotide via a cleavable linker. In embodiments, the sequencing reaction mixture includes a buffer, DNA polymerase, detergent (e.g., Triton X), a chelator (e.g., EDTA), and/or salts (e.g., ammonium sulfate, magnesium chloride, sodium chloride, or potassium chloride).

[0166] In embodiments, the kit includes, without limitation, nucleic acid primers, probes, adapters, enzymes, and the like, and are each packaged in a container, such as, without limitation, a vial, tube or bottle, in a package suitable for commercial distribution, such as, without limitation, a box, a sealed pouch, a blister pack and a carton. The package typically contains a label or packaging insert indicating the uses of the packaged materials. As used herein, “packaging materials” includes any article used in the packaging for distribution of reagents in a kit, including without limitation containers, vials, tubes, bottles, pouches, blister packaging, labels, tags, instruction sheets and package inserts.

[0167] In addition to the above components, the subject kits may further include instructions for practicing the subject methods. These instructions may be present in the subject kits in a variety of forms, one or more of which may be present in the kit. One form in which these instructions may be present is as printed information on a suitable medium or substrate, e.g., a piece or pieces of paper on which the information is printed, in the packaging of the kit, in a package insert, etc. Yet another means would be a computer readable medium, e.g., diskette, CD, digital storage medium, etc., on which the information has been recorded. Yet another means that may be present is a website address which may be used via the Internet to access the information at a removed site. Any convenient means may be present in the kits.

[0168] Adapters and/or primers may be supplied in the kits ready for use, as concentrates- requiring dilution before use, or in a lyophilized or dried form requiring reconstitution prior to use. If required, the kits may further include a supply of a suitable diluent for dilution or reconstitution of the primers and/or adapters. Optionally, the kits may further include supplies of reagents, buffers, enzymes, and dNTPs for use in carrying out nucleic acid amplification and/or sequencing. Further components which may optionally be supplied in the kit include sequencing primers suitable for sequencing templates prepared using the methods described herein.

[0169] In embodiments, the kit can further include one or more biological stain(s) (e.g., any of the biological stains as described herein). For example, the kit can further include eosin and hematoxylin. In other examples, the kit can include a biological stain such as acridine orange, Bismarck brown, carmine, coomassie blue, crystal violet, DAPI, eosin, ethidium bromide, acid fuchsine, hematoxylin, Hoechst stains, iodine, methyl green, methylene blue, neutral red, Nile blue, Nile red, osmium tetroxide, propidium iodide, rhodamine, safranin, or any combination thereof.

[0170] In an aspect is provided a solid support comprising a plurality of cells, wherein the cells include a plurality of complexes as described herein.

III. Methods

[0171] In an aspect is provided a method of profiling a sample (e.g., a cell). In embodiments, the method includes determining information (e.g., gene and protein expression) about the transcriptome of an organism thus elucidating subcellular substances and processes while gaining valuable spatial localization information within a cell. In embodiments, the method includes simultaneously sequencing a plurality of nucleic acids, such as RNA transcripts, in situ within an optically resolved volume of a sample (e.g., a voxel). RNA transcripts are responsible for the process of converting DNA into an organism’s phenotype, thus by determining the types and quantity of RNA present in a sample (e.g., a cell), it is possible to assign a phenotype to the cell. RNA transcripts include coding RNA and non-coding RNA molecules, such as messenger RNA (mRNA), transfer RNA (tRNA), micro RNA (miRNA), small interfering RNA (siRNA), small nucleolar RNA (snoRNA), small nuclear RNA (snRNA), Piwi-interacting RNA (piRNA), enhancer RNA (eRNA), or ribosomal RNA (rRNA). In embodiments, the target is pre-mRNA. In embodiments, the target is heterogeneous nuclear RNA (hnRNA).

[0172] In embodiments, the target nucleic acid can include any nucleic acid of interest. The nucleic acid can include DNA, RNA, peptide nucleic acid, morpholino nucleic acid, locked nucleic acid, glycol nucleic acid, threose nucleic acid, mixtures thereof, and hybrids thereof. In embodiments, the nucleic acid is obtained from one or more source organisms. In some embodiments, the nucleic acid can include a selected sequence or a portion of a larger sequence. In embodiments, sequencing a portion of a nucleic acid or a fragment thereof can be used to identify the source of the nucleic acid. With reference to nucleic acids, polynucleotides and/or nucleotide sequences a “portion,” “fragment” or “region” can be at least 5 consecutive nucleotides, at least 10 consecutive nucleotides, at least 15 consecutive nucleotides, at least 20 consecutive nucleotides, at least 25 consecutive nucleotides, at least 50 consecutive nucleotides, at least 100 consecutive nucleotides, or at least 150 consecutive nucleotides.

[0173] In embodiments, the entire sequence of the target is about 1 to 3kb, and only a portion of that target (e.g., 50 to 100 nucleotides) is sequenced. In embodiments, the target is about 1 to 3kb. In embodiments, the target is about 1 to 2kb. In embodiments, the target is about Ikb. In embodiments, the target is about 2kb. In embodiments, the target is less than Ikb. In embodiments, the target is about 500 nucleotides. In embodiments, the target is about 200 nucleotides. In embodiments, the target is about 100 nucleotides. In embodiments, the target is less than 100 nucleotides. In embodiments, the target is about 5 to 50 nucleotides.

[0174] In embodiments the target is an RNA transcript. In embodiments the target is a single stranded RNA nucleic acid sequence. In embodiments, the target is an RNA nucleic acid sequence or a DNA nucleic acid sequence (e.g., cDNA). In embodiments, the target is a cDNA target nucleic acid sequence and before step i), the RNA nucleic acid sequence is reverse transcribed to generate the cDNA target nucleic acid sequence. In embodiments, reverse transcription of the RNA nucleic acid is performed with a reverse transcriptase, for example, Tth DNA polymerase or mutants thereof. In embodiments, the target is genomic DNA (gDNA), mitochondrial DNA, chloroplast DNA, episomal DNA, viral DNA, or copy DNA (cDNA). In embodiments, the target is coding RNA such as messenger RNA (mRNA), and non-coding RNA (ncRNA) such as transfer RNA (tRNA), microRNA (miRNA), small nuclear RNA (snRNA), or ribosomal RNA (rRNA). In embodiments, the target is a cancer-associated gene.

[0175] In an aspect is provided a method of detecting a nucleic acid sequence in a cell or tissue. In embodiments, detecting includes sequencing in a cell or tissue. In embodiments, the method includes contacting a cell or tissue with a probe oligonucleotide and binding an RNA binding sequence of the probe oligonucleotide to an RNA molecule, wherein the probe oligonucleotide further includes a splint binding sequence (e.g., a sequence which does not bind to the RNA molecule); extending the RNA binding sequence along the RNA molecule to form a complementary sequence including a first target sequence and a second target sequence; contacting the cell or tissue with a splint oligonucleotide and binding a first sequence of the splint oligonucleotide to the splint binding sequence and binding a second sequence of the splint oligonucleotide to the second target sequence; forming a circular polynucleotide including the first sequence, or a complement thereof, and the second sequence, or a complement thereof; amplifying the circular polynucleotide to generate an amplification product including multiple copies of the first sequence, or a complement thereof, and the second sequence, or a complement thereof; and detecting (e.g., sequencing) the amplification product. In embodiments, the method includes serially cycling through detection cycles to determine the sequence, wherein each detection cycle includes hybridizing, detecting, and removing a fluorescently labelled oligonucleotide.

[0176] In embodiments, forming the circular polynucleotide includes ligating a first end and a second end of the probe oligonucleotide together. In embodiments, ligating includes forming a covalent bond from the first end and the second end. As those of skill in the art appreciate, two nucleotide sequences that that are to ligated together will generally directly abut one another. In embodiments, forming the circular oligonucleotide includes contacting the complementary sequence with an exonuclease enzyme and generating a 3’ end, wherein the exonuclease enzyme removes a portion of the second target sequence, and ligating a 3’ end and splint binding sequence together (see for example FIG. 3D). In embodiments, forming the circular polynucleotide includes extending the splint oligonucleotide along the complementary sequence to form a complement of the first sequence and a complement of the second sequence, and ligating a first end and a second end of the splint oligonucleotide together (see for example, FIG. 3E and FIG. 3F).

[0177] In embodiments, ligating includes enzymatic ligation including a ligation enzyme (e.g., Circligase enzyme, Taq DNA Ligase, HiFi Taq DNA Ligase, T4 ligase, PBCV-1 DNA Ligase (also known as SplintR® ligase) or Ampligase DNA Ligase). Non-limiting examples of ligases include DNA ligases such as DNA Ligase I, DNA Ligase II, DNA Ligase III, DNA Ligase IV, T4 DNA ligase, T7 DNA ligase, T3 DNA Ligase, E. coli DNA Ligase, PBCV-1 DNA Ligase (also known as SplintR ligase) or a Taq DNA Ligase. In embodiments, the ligase enzyme includes a T4 DNA ligase, T4 RNA ligase 1, T4 RNA ligase 2, T3 DNA ligase or T7 DNA ligase. In embodiments, the enzymatic ligation is performed by a mixture of ligases. In embodiments, the ligation enzyme is selected from the group consisting of T4 DNA ligase, T4 RNA ligase 1, T4 RNA ligase 2, RtcB ligase, T3 DNA ligase, T7 DNA ligase, Taq DNA ligase, PBCV-1 DNA Ligase, a thermostable DNA ligase (e.g., 5’ AppDNA/RNA ligase), an ATP dependent DNA ligase, an RNA-dependent DNA ligase (e.g., SplintR® ligase), and combinations thereof. In embodiments, enzymatic ligation includes two different ligation enzymes (e.g., SplintR ligation and T4 DNA ligase, or SplintR® ligase and Taq DNA ligase). In embodiments, enzymatic ligation includes more than two different ligation enzymes.

[0178] In embodiments, ligating includes chemical ligation (e.g., enzyme-free, click-mediated ligation). In embodiments, the oligonucleotides include a first bioconjugate reactive moiety capable of bonding upon contact with a second (complementary) bioconjugate reactive moiety on each respective end. In embodiments, the oligonucleotides include an alkynyl moiety at the 3’ and an azide moiety at the 5’ end that, upon hybridization to the target nucleic acid react to form a triazole linkage during suitable reaction conditions. Reaction conditions and protocols for chemical ligation techniques that are compatible with nucleic acid amplification methods are known in the art, for example El-Sagheer, A. H., & Brown, T. (2012). Accounts of chemical research, 45(8), 1258-1267; Manuguerra l. et al. Chem Commun (Camb). 2018;54(36):4529- 4532; and Odeh, F., et al. (2019). Molecules (Basel, Switzerland) , 25(1), 3, each of which is incorporated herein by reference in their entirety.

[0179] In embodiments, prior to contacting the cell or tissue with a splint oligonucleotide, the probe oligonucleotide includes from 5’ to 3’, the splint binding sequence, the RNA binding sequence, the first target sequence, and the second target sequence. For example, see FIG. 3C.

[0180] In embodiments, amplifying the circular polynucleotide includes hybridizing a primer to the circular polynucleotide and extending the primer with a strand-displacing polymerase. In embodiments, the method further includes amplifying the circular oligonucleotide by extending an amplification primer with a polymerase (e.g., a strand-displacing polymerase), wherein the primer extension generates an extension product including multiple complements of the circular oligonucleotide, referred to as an amplicon. An amplicon typically contains multiple, tandem copies of the circularized nucleic acid molecule of the corresponding sample nucleic acid. The number of copies can be varied by appropriate modification of the reaction conditions, such as varying the number of amplification cycles, using polymerases of varying processivity in the amplification reaction, or varying the length of time that the amplification reaction is run. In embodiments, the extension product includes three or more copies of the circular oligonucleotide. In embodiments, the circular oligonucleotide is copied about 3-50 times (i.e., the extension product includes about 3 to 50 complements of the circular oligonucleotide). In embodiments, the circular oligonucleotide is copied about 50-100 times (i.e., the extension product includes about 50 to 100 complements of the circular oligonucleotide). In embodiments, the circular oligonucleotide is copied about 100-300 times (i.e., the extension product includes about 100 to 300 complements of the circular oligonucleotide). In embodiments, the method includes hybridizing an amplification primer and oligonucleotide primer in the same reaction (e.g., simultaneously). In embodiments, the oligonucleotide is extended as an amplification primer after generating the circular oligonucleotide (e.g., the 3’ end of the oligonucleotide hybridized to the circular oligonucleotide is extended with a polymerase). In embodiments, the method includes contacting the target with an amplification primer and oligonucleotide primer in the same reaction (e.g., simultaneously). In embodiments, the method includes fixing the amplification products (e.g., contacting the amplification product with formalin).

[0181] In embodiments, the amplification method includes a standard dNTP mixture including dATP, dCTP, dGTP and dTTP (for DNA) or dATP, dCTP, dGTP and dUTP (for RNA). In embodiments, the amplification method includes a mixture of standard dNTPs and modified nucleotides that contain functional moieties (e.g., bioconjugate reactive groups) that serve as attachment points to the cell or the matrix in which the cell is embedded (e.g., a hydrogel). In embodiments, the amplification method includes a mixture of standard dNTPs and modified nucleotides that contain functional moieties (e.g., bioconjugate reactive groups) that participate in the formation of a bioconjugate linker. The modified nucleotides may react and link the amplification product to the surrounding cell scaffold. For example, amplifying may include an extension reaction wherein the polymerase incorporates a modified nucleotide into the amplification product, wherein the modified nucleotide includes a bioconjugate reactive moiety (e.g., an alkynyl moiety) attached to the nucleobase. The bioconjugate reactive moiety of the modified nucleotide participates in the formation of a bioconjugate linker by reacting with a complementary bioconjugate reactive moiety present in the cell (e.g., a crosslinking agent, such as NHS-PEG-azide, or an amine moiety) thereby attaching the amplification product to the internal scaffold of the cell. In embodiments, the functional moiety can be covalently cross-linked, copolymerize with or otherwise non-covalently bound to the matrix. In embodiments, the functional moiety can react with a cross-linker. In embodiments, the functional moiety can be part of a ligand-ligand binding pair. Suitable exemplary functional moieties include an amine, acrydite, alkyne, biotin, azide, and thiol. In embodiments of crosslinking, the functional moiety is cross-linked to modified dNTP or dUTP or both. In embodiments, suitable exemplary cross-linker reactive groups include imidoester (DMP), succinimide ester (NHS), maleimide (Sulfo-SMCC), carbodiimide (DCC, EDC) and phenyl azide. Cross-linkers within the scope of the present disclosure may include a spacer moiety. In embodiments, such spacer moieties may be functionalized. In embodiments, such spacer moieties may be chemically stable. In embodiments, such spacer moieties may be of sufficient length to allow amplification of the nucleic acid bound to the matrix. In embodiments, suitable exemplary spacer moieties include polyethylene glycol, carbon spacers, photo-cleavable spacers and other spacers known to those of skill in the art and the like. In embodiments, amplification reactions include standard dNTPs and a modified nucleotide (e.g., amino-allyl dUTP, 5-TCO-PEG4-dUTP, C8-Alkyne-dUTP, 5-Azidomethyl- dUTP, 5-Vinyl-dUTP, or 5-Ethynyl dLTTP). For example, during amplification a mixture of standard dNTPs and aminoallyl deoxyuridine 5 '-triphosphate (dUTP) nucleotides may be incorporated into the amplicon and subsequently cross-linked to the cell protein matrix by using a cross-linking reagent (e.g., an amine-reactive crosslinking agent with PEG spacers, such as (PEGylated bis(sulfosuccinimidyl)suberate) (BS(PEG)9)).

[0182] In embodiments, amplifying includes incubating the circular polynucleotide with a strand-displacing polymerase for about 15 minutes to about 2 hours. In embodiments, amplifying includes incubating the circular polynucleotide with a strand-displacing polymerase for about 30 minutes to about 60 minutes. In embodiments, amplifying includes binding an amplification primer to the primer binding sequence and extending the amplification primer with a stranddisplacing polymerase.

[0183] In embodiments, the probe oligonucleotide further includes a primer binding sequence. For example, a primer binding sequence includes a nucleic acid sequence of any suitable length. In embodiments, a primer binding sequence is about or at least about 10, 15, 20, 25, 30, or more nucleotides in length. In embodiments, a primer binding sequence is 10-50, 15-30, or 20-25 nucleotides in length. The primer binding sequence may be selected such that the primer (e.g., sequencing primer) has the preferred characteristics to minimize secondary structure formation or minimize non-specific amplification, for example having a length of about 20-30 nucleotides; approximately 50% GC content, and a Tm of about 55°C to about 65°C.

[0184] In embodiments, prior to contacting the cell or tissue with a splint oligonucleotide, the method includes removing the RNA molecule. In embodiments, removing the RNA molecule includes contacting the RNA molecule with a ribonuclease. In embodiments, removing the RNA includes the use of RNase-free DNase to selectively degrade DNA, thereby simplifying the RNA removal process without directly affecting the RNA. In embodiments, removing the RNA includes employing specific variants of ribonucleases that are engineered to be less aggressive, allowing for a controlled degradation of RNA. In embodiments, removing the RNA includes utilizing RNA-binding proteins that specifically bind and sequester RNA, which can then be removed through gentle purification techniques. In embodiments, removing the RNA includes designing antisense oligonucleotides that specifically hybridize with RNA molecules and recruit RNase H for targeted degradation. In embodiments, removing the RNA includes using small interfering RNA (siRNA) or short hairpin RNA (shRNA) to specifically target and degrade RNA molecules. In embodiments, removing the RNA includes applying gentle chemical treatments that selectively degrade RNA while minimizing damage to other cellular components.

[0185] In embodiments, the method further includes detecting the amplification products. In embodiments, detecting includes binding a detection agent (e.g., a labeled probe) to the amplification product. In embodiments, the detection agent includes a fluorescently labeled probe. In embodiments, the method includes exciting and detecting the label. In embodiments, detecting includes serially contacting the amplification products with labeled probes (e.g., labeled oligonucleotides or labeled nucleotides).

[0186] The phrase “labeled probes” refers to mixture of nucleic acids that are detectably labeled, e.g., fluorescently labeled, such that the presence of the probe, as well as, any target sequence to which the probe is bound can be detected by assessing the presence of the label. In some embodiments, the probes are about 30-300 bases in length, 40-300 bases in length, or 70- 300 bases in length. In some embodiments, the probes are relatively uniform in length (e.g., an average length +/— 10 bases). The probes may be uniformly labeled based on position of label and/or number of labels within the probe. In some embodiments, the probes are single-stranded. In some embodiments, the probes are double-stranded. Additional detection probes and related properties may be found in, e.g., U.S. Pat. Pub. US 2011/0039735, which is incorporated herein by reference in its entirety. In embodiments, the method includes hybridizing a primer to the amplification product and incorporating a labeled nucleotide into the primer.

[0187] In embodiments, sequencing includes hybridizing a sequencing primer to the amplification product and incorporating one or more labeled nucleotides, and detecting the incorporated one or more labeled nucleotides so as to identify the sequence.

[0188] In embodiments, the method includes sequencing the amplification products (e.g., a plurality of different amplification products). In embodiments, sequencing includes a plurality of sequencing cycles. In embodiments, sequencing includes a plurality of rounds of sequencing cycles (e.g., a first round of 10 sequencing cycles; followed by a second round of 10 sequencing cycles). In embodiments, sequencing includes a plurality of rounds of sequencing cycles (e.g., a first round of 1 sequencing cycle; followed by a second round of 1 sequencing cycle). In embodiments, sequencing includes 20 to 100 sequencing cycles. In embodiments, sequencing includes 50 to 100 sequencing cycles. In embodiments, sequencing includes 50 to 300 sequencing cycles. In embodiments, sequencing includes 50 to 150 sequencing cycles. In embodiments, sequencing includes at least 10, 20, 30 40, or 50 sequencing cycles. In embodiments, sequencing includes at least 10 sequencing cycles. In embodiments, sequencing includes 10 to 20 sequencing cycles. In embodiments, sequencing includes 10, 11, 12, 13, 14, or 15 sequencing cycles. In embodiments, sequencing includes (a) extending a sequencing primer by incorporating a labeled nucleotide, or labeled nucleotide analogue and (b) detecting the label to generate a signal for each incorporated nucleotide or nucleotide analogue. In embodiments, prior to initiating a next round of sequencing cycles, the first sequencing primer is terminated or removed. For example, termination may occur via incorporating a non-extendable nucleotide (e.g., a ddNTP) into the first sequencing primer.

[0189] In embodiments, sequencing includes sequentially sequencing a plurality of different targets by initiating sequencing with different sequencing primers. For example, a first circularizable probe includes a first primer binding site (a nucleic acid sequence complementary to a first sequencing primer) and optionally a first barcode sequence or barcode nucleotide. In a similar manner, a second and third padlock probe include a second primer binding site (a nucleic acid sequence complementary to a second, different, sequencing primer) and a third primer binding site (a nucleic acid sequence complementary to a third, different from both Primer 1 and Primer 2, sequencing primer), respectively. During the first round of sequencing (following probe circularization and amplification according to the methods described herein), using primer 1, the probe hybridized to the first nucleic acid molecule is detected. In the second round of sequencing, primer 2 can hybridize and sequence an identifying sequence of the probe (e.g., a barcode sequence or nucleotide) hybridized to a second nucleic acid molecule. Similarly, in the third round of sequencing, primer 3 can hybridize and sequence the probe hybridized to the third nucleic acid molecule.

[0190] In embodiments, sequencing includes encoding the sequencing read into a codeword. Useful encoding schemes include those developed for telecommunications, coding theory and information theory such as those set forth in Hamming, Coding and Information Theory, 2^nd Ed. Prentice Hall, Englewood Cliffs, N.J. (1986) and Moon TK. Error Correction Coding: Mathematical Methods and Algorithms, ed. 1st Wiley: 2005., each of which are incorporated herein by reference. A useful encoding scheme uses a Hamming code. A Hamming code can provide for signal (and therefore sequencing and barcode) distinction. In this scheme, signal states detected from a series of nucleotide incorporation and detection events (i.e., while sequencing the oligonucleotide barcode) can be represented as a series of the digits to form a codeword, the codeword having a length equivalent to the number incorporation/detection events. The digits can be binary (e.g. having a value of 1 for presence of signal and a value of 0 for absence of the signal) or digits can have a higher radix (e.g., a ternary digit having a value of 1 for fluorescence at a first wavelength, a value of 2 for fluorescence at a second wavelength, and a value of 0 for no fluorescence at those wavelengths, etc.). Barcode discrimination capabilities are provided when codewords can be quantified via Hamming distances between two codewords (i.e., barcode 1 having codeword 1, and barcode 2 having codeword 2, etc.). [0191] In embodiments, generating a sequencing read includes determining the identity of the nucleotides in the template polynucleotide (or complement thereof). In embodiments, a sequencing read, e.g., a first sequencing read or a second sequencing read, includes determining the identity of a portion (e.g., 1, 2, 5, 10, 20, 50 nucleotides) of the total template polynucleotide. In embodiments the first sequencing read determines the identity of 5-10 nucleotides and the second sequencing read determines the identity of more than 5-10 nucleotides (e.g., 11 to 200 nucleotides). In embodiments the first sequencing read determines the identity of more than 5-10 nucleotides (e.g., 11 to 200 nucleotides) and the second sequencing read determines the identity of 5-10 nucleotides. In embodiments, following the generation of a sequencing read, subsequent extension is performed using a plurality of standard (e.g., non-modified) dNTPs until the complementary strand is copied. In other embodiments, following the generation of a sequencing read, subsequent extension is performed using a plurality of dideoxy nucleotide triphosphates (ddNTPs) to prevent further extension of the first sequencing read product during a second sequencing read. In embodiments, following the identification of at least 5-10 (e.g., 11 to 200 nucleotides, or up to 1000 nucleotides), subsequent extension is performed using a plurality of standard (e.g., non-modified) dNTPs until the complementary strand is copied. In embodiments, following the identification of at least 5-10 (e.g., 11 to 200 nucleotides, or up to 1000 nucleotides), subsequent extension is performed using a plurality of dideoxy nucleotide triphosphates (ddNTPs) to prevent further extension of the sequencing read product.

[0192] In embodiments, sequencing includes sequencing by synthesis, sequencing by binding, or sequencing by ligation. In embodiments, sequencing includes extending a sequencing primer by incorporating a labeled nucleotide or labeled nucleotide analogue, and detecting the label to generate a signal for each incorporated nucleotide or nucleotide analogue, wherein the sequencing primer is hybridized to the amplification product.

[0193] In an aspect is provided a method of generating a complex including a circular polynucleotide in a cell, the method including: i) hybridizing a splint oligonucleotide to an extended oligonucleotide probe, thereby forming a complex, wherein the splint oligonucleotide includes a probe sequence complement and a target sequence, wherein the probe sequence complement of the splint oligonucleotide hybridizes to a probe sequence of the extended oligonucleotide probe, wherein the target sequence of the splint oligonucleotide hybridizes to a target sequence complement of the extended oligonucleotide probe, and wherein a subject sequence complement is located between the probe sequence and the target sequence complement of the extended oligonucleotide probe; ii) extending the splint oligonucleotide of the complex along the extended oligonucleotide probe with a polymerase to generate an extended splint oligonucleotide including a complement of the subject sequence; and iii) circularizing the extended splint oligonucleotide by ligating the extended splint oligonucleotide to the splint binding sequence of the oligonucleotide probe, thereby forming the complex including the circular polynucleotide.

[0194] In an aspect is provided a method of generating a complex including a circular polynucleotide in a cell, the method including: i) hybridizing a splint oligonucleotide to an extended oligonucleotide probe, thereby forming a complex, wherein the splint oligonucleotide includes, from 5’ to 3’, a probe sequence complement, a spacer sequence, and a target sequence, wherein the extended oligonucleotide probe includes, from 5’ to 3’, a probe sequence, a target hybridization sequence, a subject sequence complement, and a target sequence complement, wherein the probe sequence complement of the splint oligonucleotide hybridizes to the probe sequence of the extended oligonucleotide probe, and wherein the target sequence of the splint oligonucleotide hybridizes to the target sequence complement of the extended oligonucleotide probe; ii) extending the splint oligonucleotide of the complex along the extended oligonucleotide probe with a polymerase to generate an extended splint oligonucleotide including, from 5’ to 3’, the probe sequence complement, the spacer sequence, the target sequence, the subject sequence, and a probe hybridization sequence; and iii) circularizing the extended splint oligonucleotide by ligating the extended splint oligonucleotide to the splint binding sequence of the oligonucleotide probe, thereby forming the complex including the circular polynucleotide.

[0195] In embodiments, prior to step i) the method further includes hybridizing an oligonucleotide probe to a target polynucleotide in a cell, the target polynucleotide including, from 5’ to 3’, the target sequence, the subject sequence, and the probe hybridization sequence, wherein the probe hybridization sequence is complementary to a 3’ end of the oligonucleotide probe, and extending the oligonucleotide probe along the target polynucleotide with a polymerase to generate the extended oligonucleotide probe.

[0196] In embodiments, the method further includes amplifying the circular polynucleotide, thereby generating an amplification product including multiple copies of the subject sequence complement. In embodiments, amplifying the circular polynucleotide includes hybridizing a primer to the circular polynucleotide and extending the primer with a strand-displacing polymerase. In embodiments, amplifying the circular polynucleotide includes contacting the complex with an exonuclease enzyme and generating a 3’ end of the extended oligonucleotide probe, wherein the exonuclease enzyme removes a portion of the complementary sequence, and extending the 3’ end with a strand-displacing polymerase. [0197] In embodiments, the probe sequence of the oligonucleotide probe further includes a primer sequence. In embodiments, amplifying further includes contacting the amplification product with an amplification primer including a primer sequence complement, hybridizing the amplification primer the primer sequence complement, and extending the amplification primer with a strand-displacing polymerase, thereby generating a second amplification product.

[0198] In embodiments, prior to step i), the method further includes removing the target polynucleotide. In embodiments, removing the target polynucleotide includes contacting the target polynucleotide with a ribonuclease. In embodiments, the ribonuclease is RNAse H.

[0199] In an aspect is provided a method of generating a complex including a circular polynucleotide in a cell, the method including: a) hybridizing a splint oligonucleotide to an extended oligonucleotide probe, thereby forming a complex, wherein the splint oligonucleotide includes, from 5’ to 3’, a probe sequence complement, a spacer sequence, and a target sequence, wherein the extended oligonucleotide probe includes, from 5’ to 3’, a probe sequence, a target hybridization sequence, a subject sequence complement, and a target sequence complement, wherein the probe sequence complement of the splint oligonucleotide hybridizes to the probe sequence of the extended oligonucleotide probe, and wherein the target sequence of the splint oligonucleotide hybridizes to the target sequence complement of the extended oligonucleotide probe; b) contacting the complex with an exonuclease enzyme and generating an extended oligonucleotide probe including a 3’ end, wherein the exonuclease enzyme removes a singlestranded portion of the complex; and c) ligating the probe sequence to the 3’ end of the extended oligonucleotide probe, thereby generating a complex including a circular oligonucleotide.

[0200] In embodiments, prior to step a) the method further includes hybridizing an oligonucleotide probe to a target polynucleotide in a cell, the target polynucleotide including, from 5’ to 3’, the target sequence, the subject sequence, and a probe hybridization sequence, wherein the probe hybridization sequence is complementary to a 3’ end of the oligonucleotide probe, and extending the oligonucleotide probe along the target polynucleotide with a polymerase to generate the extended oligonucleotide probe.

[0201] In embodiments, the target polynucleotide further includes a tail sequence at the 3’ end. In embodiments, the tail sequence is not complementary to the splint oligonucleotide. In embodiments, the tail sequence is not complementary to the oligonucleotide probe. In embodiments, the tail sequence includes about 5 to about 500 nucleotides. In embodiments, the tail sequence includes about 5 to about 50, about 25 to about 100, about 50 to about 200, or about 300 nucleotides. In embodiments, the tail sequence includes about 5, 25, 50, 100, 150, 200, 250, 300, 350, 400, 450, or 500 nucleotides. In embodiments, the tail sequence includes more than about 500 nucleotides.

[0202] In embodiments, the method further includes amplifying the circular polynucleotide, thereby generating an amplification product including multiple copies of the subject sequence. In embodiments, amplifying the circular polynucleotide includes hybridizing a primer to the circular polynucleotide and extending the primer with a strand-displacing polymerase. In embodiments, amplifying the circular polynucleotide includes contacting the complex with a strand-displacing polymerase and extending the splint oligonucleotide, thereby generating an amplification product including multiple copies of the subject sequence.

[0203] In embodiments, extending includes incubating the circular polynucleotide with a strand-displacing polymerase for about 15 minutes to about 2 hours. In embodiments, extending includes incubating the circular polynucleotide with a strand-displacing polymerase for about 30 minutes to about 60 minutes. In embodiments, extending includes incubating the circular polynucleotide with a strand-displacing polymerase for about 15, 20, 25, 30, 35, 40, 45, 50, 55, or 60 minutes. In embodiments, extending includes incubating the circular polynucleotide with a strand-displacing polymerase for about 15 minutes, 30 minutes, 45 minutes, 60 minutes, 90 minutes, 2 hours, 3 hours, or 4 hours.

[0204] In an aspect is a method of generating an amplification product in a cell, the method including: i) hybridizing an oligonucleotide probe to a target polynucleotide in a cell, the target polynucleotide including a target sequence, a subject sequence, and a probe hybridization sequence, wherein the probe hybridization sequence is complementary to a 3’ end of the oligonucleotide probe; ii) extending the oligonucleotide probe along the target polynucleotide with a polymerase to generate an extended oligonucleotide probe; iii) hybridizing a splint oligonucleotide to the extended oligonucleotide probe, thereby forming a complex, wherein the splint oligonucleotide includes a probe sequence complement and the target sequence, wherein the probe sequence complement of the splint oligonucleotide hybridizes to a probe sequence of the extended oligonucleotide probe, wherein the target sequence of the splint oligonucleotide hybridizes to a target sequence complement of the extended oligonucleotide probe, and wherein a subject sequence complement is located between the probe sequence and the target sequence complement of the extended oligonucleotide probe; iv) extending the splint oligonucleotide of the complex along the extended oligonucleotide probe with a polymerase to generate an extended splint oligonucleotide including a complement of the subject sequence; v) circularizing the extended splint oligonucleotide by ligating the extended splint oligonucleotide to the splint binding sequence of the oligonucleotide probe, thereby forming a circular polynucleotide; and vi) amplifying the circular polynucleotide, thereby generating an amplification product.

[0205] In an aspect is provided a method of generating an amplification product in a cell, the method including: a) hybridizing an oligonucleotide probe to a target polynucleotide in a cell, the target polynucleotide including, a target sequence, a subject sequence, and a probe hybridization sequence, wherein the probe hybridization sequence is complementary to a 3’ end of the oligonucleotide probe, and extending the oligonucleotide probe along the target polynucleotide with a polymerase to generate an extended oligonucleotide probe; b) hybridizing a splint oligonucleotide to the extended oligonucleotide probe, thereby forming a complex, wherein the splint oligonucleotide includes a probe sequence complement and the target sequence, wherein the probe sequence complement of the splint oligonucleotide hybridizes to a probe sequence of the extended oligonucleotide probe, wherein the target sequence of the splint oligonucleotide hybridizes to a target sequence complement of the extended oligonucleotide probe, and wherein the subject sequence complement is located between the probe sequence and the target sequence complement of the extended oligonucleotide probe; c) contacting the complex with an exonuclease enzyme and generating an extended oligonucleotide probe including a 3’ end, wherein the exonuclease enzyme removes a single-stranded portion of the complex; d) ligating the probe sequence to the 3’ end of the extended oligonucleotide probe, thereby generating a complex including a circular oligonucleotide; and e) amplifying the circular oligonucleotide, thereby generating an amplification product.

[0206] In an aspect is provided a method of generating an amplification product, the method including: i) contacting a target polynucleotide including, from 3’ to 5’, a probe hybridization sequence, a subject sequence, and a target sequence with an oligonucleotide probe including, from 5’ to 3’, a probe sequence and a target hybridization sequence, and hybridizing the target hybridization sequence to the probe hybridization sequence of the target polynucleotide; ii) extending the oligonucleotide probe along the target polynucleotide with a polymerase to generate an extended oligonucleotide probe including, from 5’ to 3’, the probe sequence, the target hybridization sequence, a subject sequence complement and a target sequence complement; iii) contacting a splint oligonucleotide including, from 5’ to 3’, a probe sequence complement, a spacer sequence, and the target sequence with the extended oligonucleotide probe, hybridizing the probe sequence complement to the probe sequence of the extended oligonucleotide probe, and hybridizing the target sequence of the splint oligonucleotide to the target sequence complement of the extended oligonucleotide probe, thereby forming a complex; iv) extending the splint oligonucleotide with a non-strand displacing polymerase to generate an extended splint oligonucleotide including, from 5’ to 3’, the probe sequence complement, the spacer sequence, the target sequence, the subject sequence, and the probe hybridization sequence; v) ligating the probe hybridization sequence to the probe sequence complement, thereby generating a circular polynucleotide; and vi) amplifying the circular polynucleotide, thereby generating an amplification product.

[0207] In embodiments, the method further includes, prior to step vi), contacting the complex with an exonuclease enzyme and generating an extended oligonucleotide probe including a 3’ end, wherein the exonuclease enzyme removes a single-stranded portion of the complex. In embodiments, amplifying includes extending the 3’ end of the extended oligonucleotide probe with a strand-displacing polymerase.

[0208] In an aspect is provided a method of generating an amplification product, the method including: a) contacting a target polynucleotide including, from 3’ to 5’, a probe hybridization sequence, a subject sequence, and a target sequence with an oligonucleotide probe including, from 5’ to 3’, a probe sequence and a target hybridization sequence, and hybridizing the target hybridization sequence to the probe hybridization sequence of the target polynucleotide; b) extending the oligonucleotide probe along the target polynucleotide with a polymerase to generate an extended oligonucleotide probe including, from 5’ to 3’, the probe sequence, the target hybridization sequence, a subject sequence complement and a target sequence complement; c) contacting a splint oligonucleotide including, from 5’ to 3’, a probe sequence complement and the target sequence with the extended oligonucleotide probe, hybridizing the probe sequence complement to the probe sequence of the extended oligonucleotide probe, and hybridizing the target sequence of the splint oligonucleotide to the target sequence complement of the extended oligonucleotide probe, thereby forming a complex; d) contacting the complex with an exonuclease enzyme and generating an extended oligonucleotide probe including a 3’ end, wherein the exonuclease enzyme removes a single-stranded portion of the complex; e) ligating the probe sequence to the 3’ end of the extended oligonucleotide probe, thereby generating a circular polynucleotide; and f) amplifying the circular polynucleotide, thereby generating an amplification product.

[0209] In embodiments, extending the splint oligonucleotide includes extending with a nonstrand displacing polymerase. In embodiments, the non-strand displacing polymerase is T4 DNA polymerase. In embodiments, the non-strand displacing polymerase is T7 DNA polymerase.

[0210] In embodiments, amplifying the circular polynucleotide includes hybridizing a primer to the circular polynucleotide and extending the primer with a strand-displacing polymerase. In embodiments, extending includes incubating the circular polynucleotide with a strand-displacing polymerase for about 15 minutes to about 2 hours. In embodiments, extending includes incubating the circular polynucleotide with a strand-displacing polymerase for about 30 minutes to about 60 minutes. In embodiments, extending further includes a plurality of deoxyribonucleotides (dNTPs), optionally modified dNTPs.

[0211] In embodiments, the target polynucleotide includes a tail sequence, wherein the tail sequence is 5’ of the target sequence. In embodiments, the target polynucleotide further includes a tail sequence at a 5’ portion. In embodiments, the tail sequence is not complementary to the splint oligonucleotide. In embodiments, the tail sequence is not complementary to the oligonucleotide probe. In embodiments, the tail sequence includes about 5 to about 500 nucleotides. In embodiments, the tail sequence includes about 5 to about 50, about 25 to about 100, about 50 to about 200, or about 300 nucleotides. In embodiments, the tail sequence includes about 5, 25, 50, 100, 150, 200, 250, 300, 350, 400, 450, or 500 nucleotides. In embodiments, the tail sequence includes more than about 500 nucleotides. In embodiments, the extended oligonucleotide further includes a tail sequence complement 3’ of the target sequence complement.

[0212] In embodiments, the target polynucleotide includes a tail sequence, wherein the tail sequence is 5’ of the target sequence, wherein the extended oligonucleotide probe further includes a tail sequence complement 3’ of the target sequence complement, and wherein prior to amplifying, the tail sequence complement (i.e., the single-stranded portion of the extended oligonucleotide probe) is removed, thereby generating an extended oligonucleotide probe including a duplexed 3’ end. In embodiments, amplifying the circular polynucleotide (i.e., the circularized splint oligonucleotide) includes extending the duplexed 3’ end of the extended oligonucleotide probe with a strand-displacing polymerase.

[0213] In embodiments, extending includes incubating the duplexed 3’ end of the extended oligonucleotide probe with a strand-displacing polymerase for about 15 minutes to about 2 hours. In embodiments, extending includes incubating the duplexed 3’ end of the extended oligonucleotide probe with a strand-displacing polymerase for about 30 minutes to about 60 minutes. In embodiments, extending includes incubating the duplexed 3’ end of the extended oligonucleotide probe with a strand-displacing polymerase for about 15 minutes, 30 minutes, 45 minutes, 60 minutes, 90 minutes, 2 hours, 3 hours, 4 hours, or more.

[0214] In embodiments, removing the tail sequence complement includes exonuclease digestion. In embodiments, the exonuclease digestion includes digestion with Exonuclease I. [0215] In embodiments, wherein amplifying the circular oligonucleotide includes extending the splint oligonucleotide with a strand-displacing polymerase. In embodiments, extending includes incubating the splint oligonucleotide with the strand-displacing polymerase for about 15 minutes to about 2 hours. In embodiments, extending includes incubating the splint oligonucleotide with the strand-displacing polymerase for about 30 minutes to about 60 minutes.

[0216] In embodiments, amplifying the circular oligonucleotide includes incubating the circular oligonucleotide with the strand-displacing polymerase (a) for about 1 minute to about 2 hours, and/or (b) at a temperature of about 20°C to about 50°C. In embodiments, amplifying the circular oligonucleotide includes incubating the circular oligonucleotide with the strand-displacing polymerase for about 1 minute to about 2 hours. In embodiments, amplifying the circular oligonucleotide includes incubating the circular oligonucleotide with the strand-displacing polymerase for about 5, about 10, about 20, about 30, about 40, about 45, about 50, about 55, or about 60 minutes. In embodiments, amplifying the circular oligonucleotide includes incubating the circular oligonucleotide with the strand-displacing polymerase for about 5 minutes. In embodiments, amplifying the circular oligonucleotide includes incubating the circular oligonucleotide with the strand-displacing polymerase for about 10 minutes. In embodiments, amplifying the circular oligonucleotide includes incubating the circular oligonucleotide with the strand-displacing polymerase for about 20 minutes. In embodiments, amplifying the circular oligonucleotide includes incubating the circular oligonucleotide with the strand-displacing polymerase for about 30 minutes. In embodiments, amplifying the circular oligonucleotide includes incubating the circular oligonucleotide with the strand-displacing polymerase for about 45 minutes. In embodiments, amplifying the circular oligonucleotide includes incubating the circular oligonucleotide with the strand-displacing polymerase for about 60 minutes.

[0217] In embodiments, amplifying the circular oligonucleotide includes incubating the circular oligonucleotide with the strand-displacing polymerase for about 1 hour to about 12 hours. In embodiments, amplifying includes incubation with the strand-displacing polymerase for about 60 seconds to about 60 minutes. In embodiments, amplifying includes incubation with the stranddisplacing polymerase for about 10 minutes to about 60 minutes. In embodiments, amplifying includes incubation with the strand-displacing polymerase for about 10 minutes to about 30 minutes. In embodiments, amplifying the circular oligonucleotide includes incubating the circular oligonucleotide with the strand-displacing polymerase for about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, or about 12 hours. In embodiments, amplifying the circular oligonucleotide includes incubating the circular oligonucleotide with the strand-displacing polymerase for more than 12 hours. [0218] In embodiments, amplifying the circular oligonucleotide includes incubating the circular oligonucleotide with the strand-displacing polymerase at a temperature of about 20°C to about 50°C. In embodiments, incubation with the strand-displacing polymerase is at a temperature of about 20°C, about 25°C, about 30°C, about 35°C, about 40°C, about 45°C, or about 50°C. In embodiments, incubation with the strand-displacing polymerase is at a temperature of about 35°C to 42°C. In embodiments, incubation with the strand-displacing polymerase is at a temperature of about 35°C, about 36°C, about 37°C, about 38°C, about 39°C, about 40°C, about 41°C, or about 42°C. In embodiments, the strand-displacing polymerase is a phi29 polymerase, a SD polymerase, a Bst large fragment polymerase, phi29 mutant polymerase, a Thermus aquaticus polymerase, or a thermostable phi29 mutant polymerase.

[0219] In embodiments, amplifying includes rolling circle amplification (RCA) or rolling circle transcription (RCT) (see, e.g., Lizardi et al., Nat. Genet. 19:225-232 (1998), which is incorporated herein by reference in its entirety). Several suitable rolling circle amplification methods are known in the art. For example, RCA amplifies a circular polynucleotide (e.g., DNA) by polymerase extension of an amplification primer complementary to a portion of the template polynucleotide. This process generates copies of the circular polynucleotide template such that multiple complements of the template sequence arranged end to end in tandem are generated (i.e., a concatemer) locally preserved at the site of the circle formation. In embodiments, the amplifying occurs at isothermal conditions. In embodiments, the amplifying includes hybridization chain reaction (HCR). HCR uses a pair of complementary, kinetically trapped hairpin oligomers to propagate a chain reaction of hybridization events, as described in Dirks, R. M., & Pierce, N. A. (2004) PNAS USA, 101(43), 15275-15278, which is incorporated herein by reference for all purposes. In embodiments, the amplifying includes branched rolling circle amplification (BRCA); e.g., as described in Fan T, Mao Y, Sun Q, et al. Cancer Sci. 2018;109:2897-2906, which is incorporated herein by reference in its entirety. In embodiments, the amplifying includes hyberbranched rolling circle amplification (HRCA). Hyperbranched RCA uses a second primer complementary to the first amplification product. This allows products to be replicated by a strand-displacement mechanism, which yields drastic amplification within an isothermal reaction (Lage et al., Genome Research 13:294-307 (2003), which is incorporated herein by reference in its entirety). In embodiments, amplifying includes polymerase extension of an amplification primer. In embodiments, the polymerase is T4, T7, Sequenase, Taq, Klenow, and Pol I DNA polymerases. SD polymerase, Bst large fragment polymerase, or a phi29 polymerase or mutant thereof. In embodiments, the strand-displacing enzyme is an SD polymerase, Bst large fragment polymerase, or a phi29 polymerase or mutant thereof. In embodiments, the strand-displacing polymerase is Bst DNA Polymerase Large Fragment, Thermus aquaticus (Taq) polymerase, or a mutant thereof. In embodiments, the strand-displacing polymerase is a phi29 polymerase, a phi29 mutant polymerase or a thermostable phi29 mutant polymerase. A “phi polymerase” (or “<I>29 polymerase”) is a DNA polymerase from the 029 phage or from one of the related phages that, like 029, contain a terminal protein used in the initiation of DNA replication. For example, phi29 polymerases include the B103, GA-1, PZA, 015, BS32, M2Y (also known as M2), Nf, Gl, Cp-1, PRD1, PZE, SFS, Cp-5, Cp-7, PR4, PR5, PR722, L17, 021, and AV-1 DNA polymerases, as well as chimeras thereof. A phi29 mutant DNA polymerase includes one or more mutations relative to naturally-occurring wild-type phi29 DNA polymerases, for example, one or more mutations that alter interaction with and/or incorporation of nucleotide analogs, increase stability, increase read length, enhance accuracy, increase phototolerance, and/or alter another polymerase property, and can include additional alterations or modifications over the wild-type phi29 DNA polymerase, such as one or more deletions, insertions, and/or fusions of additional peptide or protein sequences. Thermostable phi29 mutant polymerases are known in the art, see for example US 2014/0322759, which is incorporated herein by reference for all purposes. For example, a thermostable phi29 mutant polymerase refers to an isolated bacteriophage phi29 DNA polymerase including at least one mutation selected from the group consisting of M8R, V51A, M97T, L123S, G197D, K209E, E221K, E239G, Q497P, K512E, E515A, and F526 (relative to wild type phi29 polymerase). In embodiments, the polymerase is a phage or bacterial RNA polymerases (RNAPs). In embodiments, the polymerase is a T7 RNA polymerase. In embodiments, the polymerase is an RNA polymerase. Useful RNA polymerases include, but are not limited to, viral RNA polymerases such as T7 RNA polymerase, T3 polymerase, SP6 polymerase, and Kll polymerase; Eukaryotic RNA polymerases such as RNA polymerase I, RNA polymerase II, RNA polymerase III, RNA polymerase IV, and RNA polymerase V; and Archaea RNA polymerase.

[0220] In embodiments, the amplification method includes a standard dNTP mixture including dATP, dCTP, dGTP and dTTP (for DNA) or dATP, dCTP, dGTP and dUTP (for RNA). In embodiments, the amplification method includes a mixture of standard dNTPs and modified nucleotides that contain functional moieties (e.g., bioconjugate reactive groups) that serve as attachment points to the cell or the matrix in which the cell is embedded (e.g. a hydrogel). In embodiments, the amplification method includes a mixture of standard dNTPs and modified nucleotides that contain functional moieties (e.g., bioconjugate reactive groups) that participate in the formation of a bioconjugate linker. The modified nucleotides may react and link the amplification product to the surrounding cell scaffold. For example, amplifying may include an extension reaction wherein the polymerase incorporates a modified nucleotide into the amplification product, wherein the modified nucleotide includes a bioconjugate reactive moiety (e.g., an alkynyl moiety) attached to the nucleobase. The bioconjugate reactive moiety of the modified nucleotide participates in the formation of a bioconjugate linker by reacting with a complementary bioconjugate reactive moiety present in the cell (e.g., a crosslinking agent, such as NHS-PEG-azide, or an amine moiety) thereby attaching the amplification product to the internal scaffold of the cell. In embodiments, the functional moiety can be covalently cross-linked, copolymerize with or otherwise non-covalently bound to the matrix. In embodiments, the functional moiety can react with a cross-linker. In embodiments, the functional moiety can be part of a ligand-ligand binding pair. Suitable exemplary functional moieties include an amine, acrydite, alkyne, biotin, azide, and thiol. In embodiments of crosslinking, the functional moiety is cross-linked to modified dNTP or dUTP or both. In embodiments, suitable exemplary cross-linker reactive groups include imidoester (DMP), succinimide ester (NHS), maleimide (Sulfo-SMCC), carbodiimide (DCC, EDC) and phenyl azide. Cross-linkers within the scope of the present disclosure may include a spacer moiety. In embodiments, such spacer moieties may be functionalized. In embodiments, such spacer moieties may be chemically stable. In embodiments, such spacer moieties may be of sufficient length to allow amplification of the nucleic acid bound to the matrix. In embodiments, suitable exemplary spacer moieties include polyethylene glycol, carbon spacers, photo-cleavable spacers and other spacers known to those of skill in the art and the like. In embodiments, amplification reactions include standard dNTPs and a modified nucleotide (e.g., amino-allyl dUTP, 5-TCO-PEG4-dUTP, C8-Alkyne-dUTP, 5-Azidomethyl- dUTP, 5-Vinyl-dUTP, or 5-Ethynyl dLTTP). For example, during amplification a mixture of standard dNTPs and aminoallyl deoxyuridine 5 '-triphosphate (dUTP) nucleotides may be incorporated into the amplicon and subsequently cross-linked to the cell protein matrix by using a cross-linking reagent (e.g., an amine-reactive crosslinking agent with PEG spacers, such as (PEGylated bis(sulfosuccinimidyl)suberate) (BS(PEG)9)).

[0221] In embodiments, the circular oligonucleotide is about 100 to about 1000 nucleotides in length. In embodiments, the circular oligonucleotide is about 100, about 200, about 300, about 400, about 500, about 600, about 700, about 800, about 900, or about 1000 nucleotides in length. In embodiments, the circular oligonucleotide is greater than 1000 nucleotides in length. In embodiments, the circular oligonucleotide is about or more than about 100, 150, 200, 250, 300, 350, 400, 500, 750, 1000, or more nucleotides in length. In embodiments, the circular oligonucleotide includes a plurality of sequencing primer binding sequences. In embodiments, the circular oligonucleotide includes a plurality of different sequencing primer binding sequences. [0222] In embodiments, the oligonucleotide probe further includes a primer binding sequence 5’ of the target hybridization sequence. In embodiments, the oligonucleotide probe further includes a second primer binding sequence 3’ of the primer binding sequence. In embodiments, amplifying further includes contacting the amplification product with an amplification primer including a complementary primer binding sequence, hybridizing the amplification primer the complementary primer binding sequence, and extending the amplification primer with a strand-displacing polymerase, thereby generating a second amplification product.

[0223] In embodiments, the splint oligonucleotide, the amplification primer, or both the splint oligonucleotide and the amplification primer are immobilized to a cellular component. In embodiments, the cellular component includes a nucleic acid, a protein, a lipid, a carbohydrate, an organelle, or a membrane.

[0224] In embodiments, the target polynucleotide includes RNA. In embodiments, the target polynucleotide includes DNA. In embodiments, the target polynucleotide includes DNA and RNA.

[0225] In embodiments, the polymerase is a reverse transcriptase. Exemplary reverse transcriptases include, but are not limited to, HIV-1 reverse transcriptase from human immunodeficiency virus type 1 (PDB 1HMV), HIV-2 reverse transcriptase from human immunodeficiency virus type 2, M-MLV reverse transcriptase from the Moloney murine leukemia virus, AMV reverse transcriptase from the avian myeloblastosis virus, and Telomerase reverse transcriptase. In embodiments, the polymerase is a Thermus thermophilus (Tth) DNA polymerase or mutant thereof. In embodiments, the polymerase is a Reverse Transcription Xenopolymerase (RTX). In embodiments, the polymerase is a mutant M-MLV reverse transcriptase from the Moloney murine leukemia virus.

[0226] In embodiments, removing the target polynucleotides includes contacting the target polynucleotide with a ribonuclease. In embodiments, the ribonuclease is RNAse H.

[0227] In embodiments, the target hybridization sequence of the oligonucleotide probe is greater than 30 nucleotides. In embodiments, the target hybridization sequence of the oligonucleotide probe is about 5 to about 35 nucleotides in length. In embodiments, the target hybridization sequence is about 12 to 15 nucleotides in length. In embodiments, the target hybridization sequence is about 35 to 40 nucleotides in length to maximize specificity. In embodiments, the target hybridization sequence is greater than 12 nucleotides in length. In embodiments, the target hybridization sequence is about 5, about 10, about 15, about 20, about 25, about 30, or about 35 nucleotides in length. In embodiments, the target hybridization sequence of each oligonucleotide primer is a single stranded polynucleotide that is at least 50% complementary, at least 75% complementary, at least 85% complementary, at least 90% complementary, at least 95% complementary, at least 98%, at least 99% complementary, or 100% complementary to a portion of a target polynucleotide.

[0228] In embodiments, the target hybridization sequence of each oligonucleotide probe (e.g., each oligonucleotide probe of a plurality of oligonucleotide probe) is complementary to different portions of the same target polynucleotide. In embodiments, the target hybridization sequence of each oligonucleotide probe (e.g., each oligonucleotide probe of a plurality of oligonucleotide probes) is complementary to different portions of different target polynucleotides. In embodiments, the target hybridization sequence of each oligonucleotide probe is complementary to portions of the same target polynucleotide that are separated by about 10 to about 500 nucleotides. In embodiments, the target hybridization sequence of each oligonucleotide probe are complementary to portions of the same target polynucleotide that are separated by about 10, about 15, about 20, about 25, about 30, about 35, about 40, about 45, about 50, about 75, about 100, about 125, about 150, about 175, about 200, about 225, about 250, about 275, about 300, about 325, about 350, about 375, about 400, about 425, about 450, about 475, or about 500 nucleotides. In embodiments, the target hybridization sequence of each oligonucleotide probe is complementary to portions of the same target polynucleotide that are separated by about or more than about 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, or 500 nucleotides.

[0229] In embodiments, the probe sequence of the oligonucleotide probe is greater than 30 nucleotides. In embodiments, the probe sequence of each oligonucleotide probe is about 5 to about 35 nucleotides in length. In embodiments, the probe sequence is about 12 to 15 nucleotides in length. In embodiments, the probe sequence is about 35 to 40 nucleotides in length. In embodiments, the probe sequence is about 40 to 50 nucleotides in length. In embodiments, the probe sequence is greater than 50 nucleotides in length. In embodiments, the probe sequence is about 5, about 10, about 15, about 20, about 25, about 30, about 35, about 40, about 45, or about 50 nucleotides in length.

[0230] In embodiments, each oligonucleotide probe (e.g., each oligonucleotide probe of a plurality of oligonucleotide probes) includes a primer binding sequence (i.e., a sequence complementary to a primer, such as an amplification or sequencing primer). In embodiments, the splint oligonucleotide includes a primer binding sequence. [0231] In embodiments, each oligonucleotide probe includes about 50 to about 150 nucleotides. In embodiments, the splint oligonucleotide includes about 30 to about 150 nucleotides. In embodiments, each oligonucleotide probe includes about 50 to about 300 nucleotides. In embodiments, the splint oligonucleotide includes about 30 to about 300 nucleotides. In embodiments, the splint oligonucleotide includes about 50 to about 300 nucleotides. In embodiments, each oligonucleotide probe includes about or more than about 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, or 500 nucleotides. In embodiments, the splint oligonucleotide includes about or more than about 30, 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, or 500 nucleotides. In embodiments, each oligonucleotide probe includes less than about 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, or 500 nucleotides. In embodiments, the splint oligonucleotide includes less than about 30, 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, or 500 nucleotides.

[0232] In embodiments, each oligonucleotide probe includes about 50 to about 150 nucleotides. In embodiments, each oligonucleotide probe includes about 50 to about 300 nucleotides. In embodiments, each oligonucleotide probe includes about 50 to about 500 nucleotides. In embodiments, each oligonucleotide probe includes about or more than about 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, or 500 nucleotides. In embodiments, each oligonucleotide probe includes less than about 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, or 500 nucleotides.

[0233] In embodiments, the splint oligonucleotide includes about 30 to about 150 nucleotides. In embodiments, the splint oligonucleotide includes about 30 to about 300 nucleotides. In embodiments, the splint oligonucleotide includes about 30 to about 500 nucleotides. In embodiments, the splint oligonucleotide includes about or more than about 30, 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, or 500 nucleotides. In embodiments, the splint oligonucleotide includes less than about 30, 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, or 500 nucleotides.

[0234] In embodiments, the splint oligonucleotide includes a target sequence (e.g., a sequence that is the same, or substantially the same, as a sequence of the target polynucleotide). In embodiments, the target sequence includes about 5 to about 50 nucleotides. In embodiments, the target sequence includes about 15 to about 40 nucleotides. In embodiments, the target sequence includes about 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50 nucleotides.

[0235] In embodiments, the splint oligonucleotide includes a spacer sequence (e.g., a sequence located between the probe sequence complement and the target sequence). In embodiments, the spacer sequence includes about 5 to about 20 nucleotides. In embodiments, the spacer sequence includes about 5, 10, 15, or 20 nucleotides. In embodiments, each nucleotide of the spacer sequence is the same (e.g., all the nucleotides of the spacer sequence consist of adenine, thymine, cytosine, or guanine).

[0236] In embodiments, each oligonucleotide probe and/or splint oligonucleotide include a barcode sequence. In embodiments, the barcode (i.e., the barcode sequence) is at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 nucleotides in length. In embodiments, the barcode is 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 nucleotides in length. In embodiments, the barcode is 10 to 15 nucleotides in length. In embodiments, the barcode is at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or more nucleotides in length. In embodiments, the barcode can be at most about 300, 200, 100, 90, 80, 70, 60, 50, 40, 30, 20, 15, 12, 10, 9, 8, 7, 6, 5, 4 or fewer or more nucleotides in length. In embodiments, the barcode includes between about 5 to about 8, about 5 to about 10, about 5 to about 15, about 5 to about 20, about 10 to about 150 nucleotides. In embodiments, the barcode includes between 5 to 8, 5 to 10, 5 to 15, 5 to 20, 10 to 150 nucleotides. In embodiments, the barcode is 10 nucleotides. In embodiments, the barcode may include a unique sequence (e.g., a barcode sequence) that gives the barcode its identifying functionality. The unique sequence may be random or non-random. In embodiments, the barcode is known (i.e., the nucleic sequence is known before sequencing) and is sorted into a basis-set according to their Hamming distance. Oligonucleotide barcodes (e.g., barcode sequences included in an oligonucleotide) can be associated with a target of interest by knowing, a priori, the target of interest, such as a gene or protein. In embodiments, the barcodes further include one or more sequences capable of specifically binding a gene or nucleic acid sequence of interest. For example, in embodiments, the barcode includes a sequence capable of hybridizing to mRNA, e.g., one containing a poly-T sequence (e.g., having several T's in a row, e.g., 4, 5, 6, 7, 8, or more T's).

[0237] In embodiments, the barcode is included as part of an oligonucleotide of longer sequence length, such as a primer or a random sequence (e.g., a random N-mer). In embodiments, the barcode contains random sequences to increase the mass or size of the oligonucleotide tag. The random sequence can be of any suitable length, and there may be one or more than one present. As non-limiting examples, the random sequence may have a length of 10 to 40, 10 to 30, 10 to 20, 25 to 50, 15 to 40, 15 to 30, 20 to 50, 20 to 40, or 20 to 30 nucleotides. In embodiments, each barcode sequence is selected from a known set of barcode sequences. In embodiments, each of the known set of barcode sequences is associated with a target hybridization sequence from a known set of target hybridization sequences. In embodiments, a first barcode sequence is associated with a first target hybridization sequence, and wherein a second barcode sequence is associated with a second target hybridization sequence (e.g., wherein the second target hybridization sequence is included in an oligonucleotide targeting a different target nucleic acid than the first target hybridization sequence). In embodiments, the same barcode sequence is associated with a plurality of oligonucleotides targeting different sequences of the same target nucleic acid (e.g., the same target polynucleotide).

[0238] In embodiments, the target nucleic acid (i.e., the target polynucleotide) includes a nucleic acid sequence encoding a TCR alpha chain, a TCR beta chain, a TCR delta chain, a TCR gamma chain, or any fragment thereof (e.g., variable regions including VDJ or VJ regions, constant regions, transmembrane regions, fragments thereof, combinations thereof, and combinations of fragments thereof). In embodiments, the target nucleic acid includes a nucleic acid sequence encoding a B cell receptor heavy chain, B cell receptor light chain, or any fragment thereof (e.g., variable regions including VDJ or VJ regions, constant regions, transmembrane regions, fragments thereof, combinations thereof, and combinations of fragments thereof). In embodiments, the target nucleic acid includes a CDR3 nucleic acid sequence. In embodiments, the target nucleic acid includes a TCRA gene sequence or a TCRB gene sequence. In embodiments, the target nucleic acid includes a TCRA gene sequence and a TCRB gene sequence. In embodiments, the target nucleic acid includes sequences of various T cell receptor alpha variable genes (TRAV genes), T cell receptor alpha joining genes (TRAJ genes), T cell receptor alpha constant genes (TRAC genes), T cell receptor beta variable genes (TRBV genes), T cell receptor beta diversity genes (TRBD genes), T cell receptor beta joining genes (TRB J genes), T cell receptor beta constant genes (TRBC genes), T cell receptor gamma variable genes (TRGV genes), T cell receptor gamma joining genes (TRGJ genes), T cell receptor gamma constant genes (TRGC genes), T cell receptor delta variable genes (TRDV genes), T cell receptor delta diversity genes (TRDD genes), T cell receptor delta joining genes (TRDJ genes), or T cell receptor delta constant genes (TRDC genes).

[0239] In embodiments, the target polynucleotide includes a cancer-associated gene nucleic acid sequence, a viral nucleic acid sequence, a bacterial nucleic acid sequence, or a fungal nucleic acid sequence. In embodiments, the cancer-associated gene is a nucleic acid sequence identified within The Cancer Genome Atlas Program, accessible at www.cancer.gov/tcga.

[0240] In embodiments, the target polynucleotide includes a CD4, CD68, CD20, CD11c, CD8, HLA-DR, Ki67, CD45RO, PanCK, CD3e, CD44, CD45, HLA-A, CD14, CD56, CD57, CD19, CD2, CDla, CD107a, CD21, Pax5, FOXP3, Granzyme B, CD38, CD39, CD79a, TIGIT, TOX, TP63, S100A4, TFAM, GP100, LaminBl, CK19, CK17, GAT A3, SOX2, Bcl2, EpCAM, Caveolin, CD163, CDl lb, MPO, CD141, iNOS, PD-1, PD-L1, ICOS, TIM3, LAG3, IDO1, CD40, HLA-E, IFNG, CD69, E-cadherin, CD31, Histone H3, Beta-actin, Podoplanin, SMA, Vimentin, Collagen IV, CD34, Beta-catenin, MMP-9, ZEB1, ASCT2, Na/K ATPase, HK1, LDHA, G6PD, IDH2, GLUT1, pNRF2, ATPA5, SDHA, Citrate Synthase, CPT1A, PARP, BAK, BCL-XL, BAX, BAD, Cytochrome c, LC3B, Beclin-1, H2AX, pRPS6, PCNA, Cyclin DI, HLA- DPB1, LEF1, GAL9, CD 138, MC Tryptase, 0X40, ZAP70, CD7, ClQa, CCR6, CD 15, AXL, and/or CD227 nucleic acid sequence.

[0241] In embodiments, the target polynucleotide can include any polynucleotide of interest. The polynucleotide can include DNA, RNA, peptide nucleic acid, morpholino nucleic acid, locked nucleic acid, glycol nucleic acid, threose nucleic acid, mixtures thereof, and hybrids thereof. In embodiments, the polynucleotide is obtained from one or more source organisms. In some embodiments, the polynucleotide can include a selected sequence or a portion of a larger sequence. In embodiments, sequencing a portion of a polynucleotide or a fragment thereof can be used to identify the source of the polynucleotide. With reference to nucleic acids, polynucleotides and/or nucleotide sequences a “portion,” “fragment” or “region” can be at least 5 consecutive nucleotides, at least 10 consecutive nucleotides, at least 15 consecutive nucleotides, at least 20 consecutive nucleotides, at least 25 consecutive nucleotides, at least 50 consecutive nucleotides, at least 100 consecutive nucleotides, or at least 150 consecutive nucleotides.

[0242] In embodiments, the entire sequence of the target polynucleotide is about 1 to 3kb, and only a portion of that target (e.g., 50 to 100 nucleotides) is sequenced. In embodiments, the target polynucleotide is about 1 to 3kb. In embodiments, the target polynucleotide is about 1 to 2kb. In embodiments, the target polynucleotide is about Ikb. In embodiments, the target polynucleotide is about 2kb. In embodiments, the target polynucleotide is less than Ikb. In embodiments, the target polynucleotide is about 500 nucleotides. In embodiments, the target polynucleotide is about 200 nucleotides. In embodiments, the target polynucleotide is about 100 nucleotides. In embodiments, the target polynucleotide is less than 100 nucleotides. In embodiments, the target polynucleotide is about 5 to 50 nucleotides.

[0243] In embodiments, the target polynucleotide is an RNA nucleic acid sequence or DNA nucleic acid sequence. In embodiments, the target polynucleotide is an RNA nucleic acid sequence or DNA nucleic acid sequence from the same cell. In embodiments, the target polynucleotide is an RNA nucleic acid sequence. In embodiments, the RNA nucleic acid sequence is stabilized using known techniques in the art. For example, RNA degradation by RNase should be minimized using commercially available solutions, e.g., RNA Later®, RNA Lysis Buffer, or Keratinocyte serum-free medium). In embodiments, the target polynucleotide is messenger RNA (mRNA), transfer RNA (tRNA), micro RNA (miRNA), small interfering RNA (siRNA), small nucleolar RNA (snoRNA), small nuclear RNA (snRNA), Piwi-interacting RNA (piRNA), enhancer RNA (eRNA), or ribosomal RNA (rRNA). In embodiments, the target polynucleotide is pre-mRNA. In embodiments, the target polynucleotide is heterogeneous nuclear RNA (hnRNA). In embodiments, the target polynucleotide is mRNA, tRNA (transfer RNA), rRNA (ribosomal RNA), or noncoding RNA (such as IncRNA (long noncoding RNA)). In embodiments, the target polynucleotides are on different regions of the same RNA nucleic acid sequence.

[0244] In embodiments, the target polynucleotide includes RNA nucleic acid sequences. In embodiments the target polynucleotide is an RNA transcript. In embodiments the target polynucleotide is a single stranded RNA nucleic acid sequence. In embodiments, the target polynucleotide is an RNA nucleic acid sequence or a DNA nucleic acid sequence (e.g., cDNA). In embodiments, the target polynucleotide is a cDNA target polynucleotide nucleic acid sequence and before step a), the RNA nucleic acid sequence is reverse transcribed to generate the cDNA target polynucleotide nucleic acid sequence. In embodiments, reverse transcription of the RNA nucleic acid is performed with a reverse transcriptase, for example, Tth DNA polymerase or mutants thereof. In embodiments, the target polynucleotide is genomic DNA (gDNA), mitochondrial DNA, chloroplast DNA, episomal DNA, viral DNA, or copy DNA (cDNA). In embodiments, the target polynucleotide is coding RNA such as messenger RNA (mRNA), and non-coding RNA (ncRNA) such as transfer RNA (tRNA), microRNA (miRNA), small nuclear RNA (snRNA), or ribosomal RNA (rRNA). In embodiments, the target polynucleotide is a cancer-associated gene. In embodiments, to minimize amplification errors or bias, the target polynucleotide is not reverse transcribed to generate cDNA.

[0245] In embodiments, each oligonucleotide probe (e.g., one or more oligonucleotide probes of a plurality of oligonucleotide probes) includes locked nucleic acids (LNAs), Bis-locked nucleic acids (bisLNAs), twisted intercalating nucleic acids (TINAs), bridged nucleic acids (BNAs), 2’- O-methyl RNA:DNA chimeric nucleic acids, minor groove binder (MGB) nucleic acids, morpholino nucleic acids, C5-modified pyrimidine nucleic acids, peptide nucleic acids (PNAs), or combinations thereof. In embodiments, the circularizable oligonucleotide includes locked nucleic acids (LNAs), Bis-locked nucleic acids (bisLNAs), twisted intercalating nucleic acids (TINAs), bridged nucleic acids (BNAs), 2’-O-methyl RNA:DNA chimeric nucleic acids, minor groove binder (MGB) nucleic acids, morpholino nucleic acids, C5-modified pyrimidine nucleic acids, peptide nucleic acids (PNAs), or combinations thereof. [0246] In embodiments, each splint oligonucleotide (e.g., one or more splint oligonucleotides of a plurality of splint oligonucleotides) includes locked nucleic acids (LNAs), Bis-locked nucleic acids (bisLNAs), twisted intercalating nucleic acids (TINAs), bridged nucleic acids (BNAs), 2’- O-methyl RNA:DNA chimeric nucleic acids, minor groove binder (MGB) nucleic acids, morpholino nucleic acids, C5-modified pyrimidine nucleic acids, peptide nucleic acids (PNAs), or combinations thereof. In embodiments, the circularizable oligonucleotide includes locked nucleic acids (LNAs), Bis-locked nucleic acids (bisLNAs), twisted intercalating nucleic acids (TINAs), bridged nucleic acids (BNAs), 2’-O-methyl RNA:DNA chimeric nucleic acids, minor groove binder (MGB) nucleic acids, morpholino nucleic acids, C5-modified pyrimidine nucleic acids, peptide nucleic acids (PNAs), or combinations thereof.

[0247] In embodiments, each oligonucleotide probe includes one or more locked nucleic acid (LNA) nucleotides. In embodiments, the target hybridization sequence of each oligonucleotide probe includes one or more LNA nucleotides. In embodiments, the probe sequence of each oligonucleotide probe includes one or more LNA nucleotides. In embodiments, the sequence complementary to the probe sequence of the splint oligonucleotide (e.g., the probe sequence complement) includes one or more LNA nucleotides.

[0248] In embodiments, the target hybridization sequence of the oligonucleotide probe includes a plurality of LNAs interspersed throughout the target hybridization sequence. In embodiments, the probe sequence (or complement thereof) of the oligonucleotide probe and/or splint oligonucleotide includes a plurality of LNAs interspersed throughout the probe sequence, or complement thereof.

[0249] In embodiments, the target hybridization sequence and/or probe sequence includes Bislocked nucleic acids (bisLNAs). In embodiments, the target hybridization sequence and/or probe sequence includes twisted intercalating nucleic acids (TINAs). In embodiments, the target hybridization sequence and/or probe sequence includes bridged nucleic acids (BNAs). In embodiments, the target hybridization sequence and/or probe sequence includes 2’-O-methyl RNA:DNA chimeric nucleic acids. In embodiments, the target hybridization sequence and/or probe sequence includes minor groove binder (MGB) nucleic acids. In embodiments, the target hybridization sequence and/or probe sequence includes morpholino nucleic acids. Morpholino nucleic acids are synthetic nucleotides that have standard nucleic acid bases (e.g., adenine, guanine, cytosine, and thymine) wherein those bases are bound to methylenemorpholine rings linked through phosphorodiamidate groups instead of phosphates. Morpholino nucleic acids may be referred to as phosphorodiamidate morpholino oligomers (PMOs). In embodiments, the target hybridization sequence and/or probe sequence includes C5-modified pyrimidine nucleic acids. In embodiments, the target hybridization sequence and/or probe sequence includes peptide nucleic acids (PNAs). In embodiments, the target hybridization sequence and/or probe sequence includes from 5' to 3' a plurality of synthetic nucleotides (e.g., LNAs) followed by a plurality (e.g., 2 to 5) canonical or native nucleotides (e.g., dNTPs). In embodiments, the target hybridization sequence and/or probe sequence includes one or more (e.g., 2 to 5) deoxyuracil nucleobases (dU). In embodiments, the one or more dU nucleobases are at or near the 3’ end of the target hybridization sequence and/or probe sequence (e.g., within 5 nucleotides of the 3’ end). In embodiments, the target hybridization sequence and/or probe sequence includes from 5' to 3' a plurality (e.g., 2 to 5) of phosphorothioate nucleic acids, followed by a plurality of synthetic nucleotides (e.g., LNAs), and subsequently followed by a plurality (e.g., 2 to 5) of canonical nucleobases. In some embodiments, the target hybridization sequence and/or probe sequence includes a plurality of canonical nucleobases, wherein the canonical nucleobases terminate (i.e., at the 3' end) with a deoxyuracil nucleobase (dU).

[0250] In embodiments, the target hybridization sequence and/or probe sequence includes a plurality of LNAs interspersed throughout the polynucleotide. In embodiments, the target hybridization sequence and/or probe sequence includes a plurality of consecutive LNAs (e.g., 2 to 5 LNAs, 5 to 7 LNAs, or 7 to 10 LNAs) throughout the target hybridization sequence and/or probe sequence. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes less than 70%, less than 60%, less than 50%, less than 40%, less than 30%, less than 20%, less than 10%, or less than 5% of LNAs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes up to about 70%, up to about 60%, up to about 50%, up to about 40%, up to about 30%, up to about 20%, up to about 10%, or up to about 5% of LNAs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes more than 60%, more than 50%, more than 40%, more than 30%, more than 20%, more than 10%, or more than 5% of LNAs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 5% to about 10%, about 10% to about 20%, about 20% to about 30%, about 30% to about 40%, about 40% to about 50%, about 50% to about 60%, or about 60% to about 70% of LNAs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 5%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, or about 70% of LNAs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, or about 95% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes less than 95%, less than 90%, less than 80%, less than 70%, less than 60%, less than 50%, less than 40%, or less than 30% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes up to about 95%, up to about 90%, up to about 80%, up to about 70%, up to about 60%, up to about 50%, up to about 40%, or up to about 30% of canonical dNTPs. In embodiments, the entire composition of the the target hybridization sequence and/or probe sequence includes more than 90%, more than 80%, more than 70%, more than 60%, more than 50%, more than 40%, or more than 30% of canonical dNTPs.

[0251] In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 70% of LNAs and about 30% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 65% of LNAs and about 35% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 60% of LNAs and about 40% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 55% of LNAs and about 45% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 50% of LNAs and about 50% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 45% of LNAs and about 55% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 40% of LNAs and about 60% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 35% of LNAs and about 65% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 30% of LNAs and about 70% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 25% of LNAs and about 75% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 20% of LNAs and about 80% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 15% of LNAs and about 85% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 10% of LNAs and about 90% of canonical dNTPs. In embodiments, the entire composition of the target hybridization sequence and/or probe sequence includes about 5% of LNAs and about 95% of canonical dNTPs.

[0252] In embodiments, the targets are proteins or carbohydrates. In embodiments, the targets are proteins. In embodiments, the targets are carbohydrates. In embodiments when the target are proteins and/or carbohydrates, the method includes contacting the proteins with a specific binding reagent, wherein the specific binding reagent includes an oligonucleotide barcode (e.g., the target polynucleotide is attached to the specific binding reagent). In embodiments, the specific binding reagent includes an antibody, single-chain Fv fragment (scFv), antibody fragment-antigen binding (Fab), or an aptamer. In embodiments, the specific binding reagent is a peptide, a cell penetrating peptide, an aptamer, a DNA aptamer, an RNA aptamer, an antibody, an antibody fragment, a light chain antibody fragment, a single-chain variable fragment (scFv), a lipid, a lipid derivative, a phospholipid, a fatty acid, a triglyceride, a glycerolipid, a glycerophospholipid, a sphingolipid, a saccharolipid, a polyketide, a polylysine, polyethyleneimine, diethylaminoethyl (DEAE)-dextran, cholesterol, or a sterol moiety. In embodiments, the specific binding reagent interacts (e.g., contacts, or binds) with one or more specific binding reagents on the cell surface. Carbohydratespecific antibodies are known in the art, see for example Kappler, K., Hennet, T. Genes Immun 21, 224-239 (2020)In embodiments, the target polynucleotide is polynucleotide attached to a specific binding reagent. In embodiments, the specific binding reagent is an antibody, single-chain Fv fragment (scFv), antibody fragment-antigen binding (Fab), or an aptamer.

[0253] In embodiments, the target polynucleotide is attached to a specific binding reagent (e.g., an antibody) via a linker (e.g., a bioconjugate linker). In embodiments, the target polynucleotide is attached to the specific binding reagent via a linker formed by reacting a first bioconjugate reactive moiety (e.g., the bioconjugate reactive moiety includes an amine moiety, aldehyde moiety, alkyne moiety, azide moiety, carboxylic acid moiety, dibenzocyclooctyne (DBCO) moiety, tetrazine moiety, epoxy moiety, isocyanate moiety, furan moiety, maleimide moiety, thiol moiety, or transcyclooctene (TCO) moiety) with a second bioconjugate reactive moiety). In embodiments, the target polynucleotide includes a barcode, wherein the barcode is a known sequence associated with the specific binding reagent. In embodiments, the barcode is at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 nucleotides in length. In embodiments, the barcode is 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 nucleotides in length.

[0254] Specific antibodies tagged with known oligonucleotide sequences can be synthesized by using bifunctional crosslinkers reactive towards thiol (via maleimide) and amine (via NHS) moieties. For example, a 5’-thiol-modified oligonucleotide could be conjugated to a crosslinker via mal eimide chemistry and purified. The oligos with a 5’-NHS-ester would then be added to a solution of antibodies and reacted with amine residues on the antibodies surface to generate tagged antibodies capable of binding analytes with target epitopes. These tagged antibodies include oligonucleotide sequence(s). The one or more oligonucleotide sequences may include a barcode, binding sequences (e.g., primer binding sequence or sequences complementary to hybridization pads), and/or unique molecular identifier (UMI) sequences.

[0255] In embodiments, specific binding entails a binding affinity, expressed as a KD (such as a KD measured by surface plasmon resonance at an appropriate temperature, such as 37° C). In embodiments, the KD of a specific binding interaction is less than about 100 nM, 50 nM, 10 nM, 1 nM, 0.05 nM, or lower. In embodiments, the KD of a specific binding interaction is about 0.01- 100 nM, 0.1-50 nM, or 1-10 nM. In embodiments, the KD of a specific binding interaction is less than 10 nM. The binding affinity of an antibody can be readily determined by one of ordinary skill in the art (for example, by Scatchard analysis). A variety of immunoassay formats can be used to select antibodies specifically immunoreactive with a particular antigen. For example, solid-phase ELISA immunoassays are routinely used to select monoclonal antibodies specifically immunoreactive with an analyte. See Harlow and Lane, ANTIBODIES: A LABORATORY MANUAL, Cold Springs Harbor Publications, New York, (1988) for a description of immunoassay formats and conditions that can be used to determine specific immunoreactivity. Typically, a specific or selective reaction will be at least twice background signal to noise and more typically more than 10 to 100 times greater than background.

[0256] In embodiments, the methods and compositions described herein are utilized to analyze the various sequences of TCRs and BCRs from immune cells, for example various clonotypes. In embodiments, the target nucleic acid includes a nucleic acid sequence encoding a TCR alpha chain, a TCR beta chain, a TCR delta chain, a TCR gamma chain, or any fragment thereof (e.g., variable regions including VDJ or VJ regions, constant regions, transmembrane regions, fragments thereof, combinations thereof, and combinations of fragments thereof). In embodiments, the target nucleic acid includes a nucleic acid sequence encoding a B cell receptor heavy chain, B cell receptor light chain, or any fragment thereof (e.g., variable regions including VDJ or VJ regions, constant regions, transmembrane regions, fragments thereof, combinations thereof, and combinations of fragments thereof). In embodiments, the target nucleic acid includes a CDR3 nucleic acid sequence. In embodiments, the target nucleic acid includes a TCRA gene sequence or a TCRB gene sequence. In embodiments, the target nucleic acid includes a TCRA gene sequence and a TCRB gene sequence. In embodiments, the target nucleic acid includes sequences of various T cell receptor alpha variable genes (TRAV genes), T cell receptor alpha joining genes (TRAJ genes), T cell receptor alpha constant genes (TRAC genes), T cell receptor beta variable genes (TRBV genes), T cell receptor beta diversity genes (TRBD genes), T cell receptor beta joining genes (TRBJ genes), T cell receptor beta constant genes (TRBC genes), T cell receptor gamma variable genes (TRGV genes), T cell receptor gamma joining genes (TRGJ genes), T cell receptor gamma constant genes (TRGC genes), T cell receptor delta variable genes (TRDV genes), T cell receptor delta diversity genes (TRDD genes), T cell receptor delta joining genes (TRDJ genes), or T cell receptor delta constant genes (TRDC genes).

[0257] RNA, including mRNA, is highly susceptible to degradation upon exposure to one or more RNAses. RNAses are present in a wide range of locations, including water, many reagents, laboratory equipment and surfaces, skin, and mucous membranes. Working with RNA often requires preparing an RNAse-free environment and materials, as well as taking precautions to avoid introducing RNAses into an RNAse-free environment. These precautions include, but are not limited to, cleaning surfaces with an RNAse cleaning product (e.g., RNASEZAP™ and other commercially available products or 0.5% sodium dodecyl sulfate [SDS] followed by 3% H2O2); using a designated workspace, materials, and equipment (e.g., pipets, pipet tips); using barrier tips; baking designated glassware (e.g., 300° C. for 2 hours) prior to use; treating enzymes, reagents, and other solutions (e.g., with diethyl pyrocarbonate [DEPC] or dimethyl pyrocarbonate [DMPC]) or using commercially available, certified RNAse-free water or solutions, or ultrafiltered water (e.g., for Tris-based solutions); including an RNAse inhibitor while avoiding temperatures or denaturing conditions that could deactivate the inhibitor); and wearing clean gloves (while avoiding contaminated surfaces) and a clean lab coat.

[0258] In embodiments, the cell forms part of a tissue in situ. In embodiments, the cell is an isolated single cell. In embodiments, the cell is a prokaryotic cell. In embodiments, the cell is a eukaryotic cell. In embodiments, the cell is a bacterial cell (e.g., a bacterial cell or bacterial spore), a fungal cell (e.g., a fungal spore), a plant cell, or a mammalian cell. In embodiments, the cell is a stem cell. In embodiments, the stem cell is an embryonic stem cell, a tissue-specific stem cell, a mesenchymal stem cell, or an induced pluripotent stem cell. In embodiments, the cell is an endothelial cell, muscle cell, myocardial, smooth muscle cell, skeletal muscle cell, mesenchymal cell, epithelial cell; hematopoietic cell, such as lymphocytes, including T cell, e.g., (Thl T cell, Th2 T cell, ThO T cell, cytotoxic T cell); B cell, pre-B cell; monocytes; dendritic cell; neutrophils; or a macrophage. In embodiments, the cell is a stem cell, an immune cell, a cancer cell (e.g., a circulating tumor cell or cancer stem cell), a viral-host cell, or a cell that selectively binds to a desired target. In embodiments, the cell includes a T cell receptor gene sequence, a B cell receptor gene sequence, or an immunoglobulin gene sequence. In embodiments, the cell includes a Toll-like receptor (TLR) gene sequence. In embodiments, the cell includes a gene sequence corresponding to an immunoglobulin light chain polypeptide and a gene sequence corresponding to an immunoglobulin heavy chain polypeptide. In embodiments, the cell is a genetically modified cell. In embodiments, the cell is a circulating tumor cell or cancer stem cell.

[0259] In embodiments, the cell is a prokaryotic cell. In embodiments, the cell is a bacterial cell. In embodiments, the bacterial cell is a Bacteroides, Clostridium, Faecalibacterium, Eubacterium, Ruminococcus, Peptococcus, Peptostreptococcus, o Bifidobacterium cell. In embodiments, the bacterial cell is a Bacteroides fragilis, Bacteroides melaninogenicus, Bacteroides oralis, Enterococcus faecalis, Escherichia coli, Enterobacter sp., Klebsiella sp., Bifidobacterium bifidum, Staphylococcus aureus, Lactobacillus, Clostridium perfringens, Proteus mirabilis, Clostridium tetani, Clostridium septicum, Pseudomonas aeruginosa, Salmonella enterica, Faecalibacterium prausnitzii, Peptostreptococcus sp., or Peptococcus sp. cell. In embodiments, the cell is a fungal cell. In embodiments, the fungal cell is a Candida, Saccharomyces, Aspergillus, Penicillium, Rhodotorula, Trametes, Pleospora, Sclerotinia, Bullera, or a Galactomyces cell.

[0260] In embodiments, the cell is a viral-host cell. A “viral-host cell” is used in accordance with its ordinary meaning in virology and refers to a cell that is infected with a viral genome (e.g., viral DNA or viral RNA). The cell, prior to infection with a viral genome, can be any cell that is susceptible to viral entry. In embodiments, the viral-host cell is a lytic viral-host cell. In embodiments, the viral-host cell is capable of producing viral protein. In embodiments, the viral- host cell is a lysogenic viral-host cell. In embodiments, the cell is a viral-host cell including a viral nucleic acid sequence, wherein the viral nucleic acid sequence is from a Hepadnaviridae, Adenoviridae , Herpesviridae, Poxviridae, Parvoviridae, Reoviridae, Coronaviridae , Retroviridae virus.

[0261] In embodiments, the cell is an adherent cell (e.g., epithelial cell, endothelial cell, or neural cell). Adherent cells are usually derived from tissues of organs and attach to a substrate (e.g., epithelial cells adhere to an extracellular matrix coated substrate via transmembrane adhesion protein complexes). Adherent cells typically require a substrate, e.g., tissue culture plastic, which may be coated with extracellular matrix (e.g., collagen and laminin) components to increase adhesion properties and provide other signals needed for growth and differentiation. In embodiments, the cell is a neuronal cell, an endothelial cell, epithelial cell, germ cell, plasma cell, a muscle cell, peripheral blood mononuclear cell (PBMC), a myocardial cell, or a retina cell. In embodiments, the cell is a suspension cell (e.g., a cell free-floating in the culture medium, such a lymphoblast or hepatocyte). In embodiments, the cell is a glial cell (e.g., astrocyte, radial glia), pericyte, or stem cell (e.g., a neural stem cell). In embodiments, the cell is a neuronal cell. In embodiments, the cell is an endothelial cell. In embodiments, the cell is an epithelial cell. In embodiments, the cell is a germ cell. In embodiments, the cell is a plasma cell. In embodiments, the cell is a muscle cell. In embodiments, the cell is a peripheral blood mononuclear cell (PBMC). In embodiments, the cell is a myocardial cell. In embodiments, the cell is a retina cell. In embodiments, the cell is a lymphoblast. In embodiments, the cell is a hepatocyte. In embodiments, the cell is a glial cell. In embodiments, the cell is an astrocyte. In embodiments, the cell is a radial glia. In embodiments, the cell is a pericyte. In embodiments, the cell is a stem cell. In embodiments, the cell is a neural stem cell.

[0262] In embodiments, the cell is bound to a known antigen. In embodiments, the cell is a cell that selectively binds to a desired target, wherein the target is an antibody, or antigen binding fragment, an aptamer, affimer, non-immunoglobulin scaffold, small molecule, or genetic modifying agent. In embodiments, the cell is a leukocyte (i.e., a white-blood cell). In embodiments, leukocyte is a granulocyte (neutrophil, eosinophil, or basophil), monocyte, or lymphocyte (T cells and B cells). In embodiments, the cell is a lymphocyte. In embodiments, the cell is a T cell, an NK cell, or a B cell.

[0263] In embodiments, the cell is an immune cell. In embodiments, the immune cell is a granulocyte, a mast cell, a monocyte, a neutrophil, a dendritic cell, or a natural killer (NK) cell. In embodiments, the immune cell is an adaptive cell, such as a T cell, NK cell, or a B cell. In embodiments, the cell includes a T cell receptor gene sequence, a B cell receptor gene sequence, or an immunoglobulin gene sequence. In embodiments, the immune cell is a granulocyte. In embodiments, the immune cell is a mast cell. In embodiments, the immune cell is a monocyte. In embodiments, the immune cell is a neutrophil. In embodiments, the immune cell is a dendritic cell. In embodiments, the immune cell is a natural killer (NK) cell. In embodiments, the immune cell is a T cell. In embodiments, the immune cell is a B cell. In embodiments, the cell includes a T cell receptor gene sequence. In embodiments, the cell includes a B cell receptor gene sequence. In embodiments, the cell includes an immunoglobulin gene sequence. In embodiments, the plurality of target nucleic acids includes non-contiguous regions of a nucleic acid molecule. In embodiments, the non-contiguous regions include regions of a VDJ recombination of a B cell or T cell.

[0264] In embodiments, the cell is a cancer cell. In embodiments, the cancer is lung cancer, colorectal cancer, skin cancer, colon cancer, pancreatic cancer, breast cancer, cervical cancer, lymphoma, leukemia, or a cancer associated with aberrant K-Ras, aberrant APC, aberrant Smad4, aberrant p53, or aberrant TGFp. In embodiments, the cancer cell includes ERBB2, KRAS, TP53, PIK3CA, or FGFR2 gene. In embodiments, the cancer cell includes a HER2 gene. In embodiments, the cancer cell includes a cancer-associated gene (e.g., an oncogene associated with kinases and genes involved in DNA repair) or a cancer-associated biomarker. A “biomarker” is a substance that is associated with a particular characteristic, such as a disease or condition. A change in the levels of a biomarker may correlate with the risk or progression of a disease or with the susceptibility of the disease to a given treatment. In embodiments, the cancer is Acute Myeloid Leukemia, Adrenocortical Carcinoma, Bladder Urothelial Carcinoma, Breast Ductal Carcinoma, Breast Lobular Carcinoma, Cervical Carcinoma, Cholangiocarcinoma, Colorectal Adenocarcinoma, Esophageal Carcinoma, Gastric Adenocarcinoma, Glioblastoma Multiforme, Head and Neck Squamous Cell Carcinoma, Hepatocellular Carcinoma, Kidney Chromophobe Carcinoma, Kidney Clear Cell Carcinoma, Kidney Papillary Cell Carcinoma, Lower Grade Glioma, Lung Adenocarcinoma, Lung Squamous Cell Carcinoma, Mesothelioma, Ovarian Serous Adenocarcinoma, Pancreatic Ductal Adenocarcinoma, Paraganglioma & Pheochromocytoma, Prostate Adenocarcinoma, Sarcoma, Skin Cutaneous Melanoma, Testicular Germ Cell Cancer, Thymoma, Thyroid Papillary Carcinoma, Uterine Carcinosarcoma, Uterine Corpus Endometrioid Carcinoma, or Uveal Melanoma. In embodiments, the cancer-associated gene is a nucleic acid sequence identified within The Cancer Genome Atlas Program, accessible at www.cancer.gov/tcga.

[0265] In embodiments, the cancer-associated biomarker is MDC, NME-2, KGF, P1GF, Flt-3L, HGF, MCP1, SAT-1, MIP-l-b, GCLM, OPG, TNF RII, VEGF-D, IT AC, MMP-10, GPI, PPP2R4, AKR1B1, Amyl A, MIP-lb, P-Cadherin, or EPO. In embodiments, the cancer- associated gene is a AKT1, AKT2, AKT3, ALK, AR, ARAF, ARID1A, ATM, ATR, ATRX, AXL, BAP1, BRAF, BRCA1, BRCA2, BTK, CBL, CCND1, CCND2, CCND3, CCNE1, CDK12, CDK2, CDK4, CDK6, CDKN1B, CDKN2A, CDKN2B, CHEK1, CHEK2, CREBBP, CSF1R, CTNNB1, DDR2, EGFR, ERBB2, ERBB3, ERBB4, ERCC2, ERG, ESRI, ETV1, ETV4, ETV5, EZH2, FANCA, FANCD2, FANCI, FBXW7, FGF19, FGF3, FGFR1, FGFR2, FGFR3, FGFR4, FGR, FLT3, FOXL2, GATA2, GNA11, GNAQ, GNAS, H3F3A, HIST1H3B, HNF1A, HRAS, IDH1, IDH2, IGF1R, JAK1, JAK2, JAK3, KDR, KIT, KNSTRN, KRAS, MAGOH, MAP2K1, MAP2K2, MAP2K4, MAPK1, MAX, MDM2, MDM4, MED12, MET, MLH1, MRE11 A, MSH2, MSH6, MTOR, MYB, MYBL1, MYC, MYCL, MYCN, MYD88, NBN, NF1, NF2, NFE2L2, NOTCH1, NOTCH2, NOTCH3, NOTCH4, NRAS, NRG1, NTRK1, NTRK2, NTRK3, NUTM1, PALB2, PDGFRA, PDGFRB, PIK3CA, PIK3CB, PIK3R1, PMS2, POLE, PPARG, PPP2R1A, PRKACA, PRKACB, PTCHI, PTEN, PTPN11, RAC1, RAD50, RAD51, RAD51B, RAD51C, RAD51D, RAFI, RBI, RELA, RET, RHEB, RHOA, RICTOR, RNF43, ROS1, RSPO2, RSPO3, SETD2, SF3B1, SLX4, SMAD4, SMARCA4, SMARCB1, SMO, SPOP, SRC, STAT3, STK11, TERT, TOPI, TP53, TSC1, TSC2, U2AF1, or XPO1 gene. In embodiments, the cancer- associated gene is a ABL1, AKT1, ALK, APC, ATM, BRAF, CDH1, CDKN2A, CSF1R, CTNNB1, EGFR, ERBB2, ERBB4, EZH2, FBXW7, FGFR1, FGFR2, FGFR3, FLT3, GNA11, GNAQ, GNAS, HNF1A, HRAS, IDH1, IDH2, JAK2, JAK3, KDR, KIT, KRAS, MET, MLH1, MPL, NOTCH1, NPM1, NRAS, PDGFRA, PIK3CA, PTEN, PTPN11, RBI, RET, SMAD4, SMARCB1, SMO, SRC, STK11, TP53, or VHL gene. In embodiments, the cell is a cell (e.g., a T cell) within a tumor. In embodiments, the cell is a non-allogenic cell (i.e., native cell to the subject) within a tumor. In embodiments, the cell is a tumor infiltrating lymphocyte (TIL). In embodiments, the cell is an allogenic cell. In embodiments, the cell is a circulating tumor cell.

[0266] In embodiments, the cell in situ is obtained from a subject (e.g., human or animal tissue). Once obtained, the cell is placed in an artificial environment in plastic or glass containers supported with specialized medium containing essential nutrients and growth factors to support proliferation. In embodiments, the cell (and/or the tissue) is permeabilized and immobilized to a solid support surface. In embodiments, the cell (and/or the tissue) is permeabilized and immobilized to an array (i.e., to discrete locations arranged in an array). In embodiments, the cell is immobilized to a solid support surface. In embodiments, the surface includes a patterned surface (e.g., suitable for immobilization of a plurality of cells in an ordered pattern. The discrete regions of the ordered pattern may have defined locations in a regular array, which may correspond to a rectilinear pattern, circular pattern, hexagonal pattern, or the like. These discrete regions are separated by interstitial regions. As used herein, the term “interstitial region” refers to an area in a substrate or on a surface that separates other areas of the substrate or surface. In embodiments, a plurality of cells are immobilized on a patterned surface that have a mean or median separation from one another of about 10-20 pm. In embodiments, a plurality of cells are immobilized on a patterned surface that have a mean or median separation from one another of about 10-20; 10-50; or 100 pm. In embodiments, a plurality of cells are arrayed on a substrate. In embodiments, a plurality of cells are immobilized in a 96-well microplate having a mean or median well-to-well spacing of about 8 mm to about 12 mm (e.g., about 9 mm). In embodiments, a plurality of cells are immobilized in a 384-well microplate having a mean or median well-to- well spacing of about 3 mm to about 6 mm (e.g., about 4.5 mm).

[0267] In embodiments, the cell is attached to the substrate via a bioconjugate reactive linker. In embodiments, the cell is attached to the substrate via a specific binding reagent. In embodiments, the specific binding reagent includes an antibody, single-chain Fv fragment (scFv), antibody fragment-antigen binding (Fab), or an aptamer. In embodiments, the specific binding reagent includes an antibody, or antigen binding fragment, an aptamer, affimer, or nonimmunoglobulin scaffold. In embodiments, the specific binding reagent is a peptide, a cell penetrating peptide, an aptamer, a DNA aptamer, an RNA aptamer, an antibody, an antibody fragment, a light chain antibody fragment, a single-chain variable fragment (scFv), a lipid, a lipid derivative, a phospholipid, a fatty acid, a triglyceride, a glycerolipid, a glycerophospholipid, a sphingolipid, a saccharolipid, a polyketide, a polylysine, polyethyleneimine, diethylaminoethyl (DEAE)-dextran, cholesterol, or a sterol moiety. Substrates may be prepared for selective capture of particular cells. For example, a substrate containing a plurality of bioconjugate reactive moieties or a plurality of specific binding reagents, optionally in an ordered pattern, contacts a plurality of cells. Only cells containing complementary bioconjugate reactive moieties or complementary specific binding reagents are capable of reacting, and thus adhering, to the substrate.

[0268] In embodiments, the cell is permeabilized. In embodiments, the methods are performed in situ on isolated cells or in tissue sections that have been prepared according to methodologies known in the art. Methods for permeabilization and fixation of cells and tissue samples are known in the art, as exemplified by Cremer et al., The Nucleus: Volume 1 : Nuclei and Subnuclear Components, R. Hancock (ed.) 2008; and Larsson et al., Nat. Methods (2010) 7:395-397, the content of each of which is incorporated herein by reference in its entirety. In embodiments, the cell is cleared (e.g., digested) of proteins, lipids, or proteins and lipids. In embodiments, the method includes digesting the cell by contacting the cell with an endopeptidase.

[0269] In embodiments, the cell is immobilized to a substrate. The cell may have been cultured on the surface, or the cell may have been initially cultured in suspension and then fixed to the surface. Substrates can be two- or three-dimensional and can include a planar surface (e.g., a glass slide). A substrate can include glass (e.g., controlled pore glass (CPG)), quartz, plastic (such as polystyrene (low cross-linked and high cross-linked polystyrene), polycarbonate, polypropylene and poly(methymethacrylate)), acrylic copolymer, polyamide, silicon, metal (e.g., alkanethiolate- derivatized gold), cellulose, nylon, latex, dextran, gel matrix (e.g., silica gel), polyacrolein, or composites. In embodiments, the substrate includes a polymeric coating, optionally containing bioconjugate reactive moieties capable of affixing the sample. Suitable three-dimensional substrates include, for example, spheres, microparticles, beads, membranes, slides, plates, micromachined chips, tubes (e.g., capillary tubes), microwells, microfluidic devices, channels, filters, or any other structure suitable for anchoring a sample. In embodiments, the substrate is not a flow cell. In embodiments, the substrate includes a polymer matrix material (e.g., polyacrylamide, cellulose, alginate, polyamide, cross-linked agarose, cross-linked dextran or cross-linked polyethylene glycol), which may be referred to herein as a “matrix”, “synthetic matrix”, “exogenous polymer” or “exogenous hydrogel”. In embodiments, a matrix may refer to the various components and organelles of a cell, for example, the cytoskeleton (e.g., actin and tubulin), endoplasmic reticulum, Golgi apparatus, vesicles, etc. In embodiments, the matrix is endogenous to a cell. In embodiments, the matrix is exogenous to a cell. In embodiments, the matrix includes both the intracellular and extracellular components of a cell. In embodiments, polynucleotide primers may be immobilized on a matrix including the various components and organelles of a cell. Immobilization of polynucleotide primers on a matrix of cellular components and organelles of a cell is accomplished as described herein, for example, through the interaction/reaction of complementary bioconjugate reactive moieties. In embodiments, the exogenous polymer may be a matrix or a network of extracellular components that act as a point of attachment (e.g., act as an anchor) for the cell to a substrate.

[0270] In embodiments, the cell is exposed to paraformaldehyde (i.e., by contacting the cell with paraformaldehyde). Any suitable permeabilization and fixation technologies can be used for making the cell available for the detection methods provided herein. In embodiments the method includes affixing single cells or tissues to a transparent substrate. Exemplary tissue include those from skin tissue, muscle tissue, bone tissue, organ tissue and the like. In embodiments, the method includes immobilizing the cell in situ to a substrate and permeabilized for delivering probes, enzymes, nucleotides and other components required in the reactions. In embodiments, the cell includes many cells from a tissue section in which the original spatial relationships of the cells are retained. In embodiments, the cell in situ is within a Formalin-Fixed Paraffin-Embedded (FFPE) sample. In embodiments, the cell is subjected to paraffin removal methods, such as methods involving incubation with a hydrocarbon solvent, such as xylene or hexane, followed by two or more washes with decreasing concentrations of an alcohol, such as ethanol. The cell may be rehydrated in a buffer, such as PBS, TBS or MOPs. In embodiments, the FFPE sample is incubated with xylene and washed using ethanol to remove the embedding wax, followed by treatment with Proteinase K to permeabilized the tissue. In embodiments, the cell is fixed with a chemical fixing agent. In embodiments, the chemical fixing agent is formaldehyde or glutaraldehyde. In embodiments, the chemical fixing agent includes both formaldehyde and glutaraldehyde. In embodiments, the chemical fixing agent is glyoxal or dioxolane. In embodiments, the chemical fixing agent includes one or more of ethanol, methanol, 2-propanol, acetone, and glyoxal. In embodiments, the chemical fixing agent includes formalin, Greenfix®, Greenfix® Plus, UPM, CyMol®, HOPE®, CytoSkelFix™, F-Solv®, FineFIX®, RCL2/KINFix, UMFIX, Glyo-Fixx®, Histochoice®, or PAXgene®. In embodiments, the cell is fixed within a synthetic three-dimensional matrix (e.g., polymeric material). In embodiments, the synthetic matrix includes polymeric-crosslinking material. In embodiments, the material includes polyacrylamide, poly-ethylene glycol (PEG), poly(acrylate-co-acrylic acid) (PAA), or Poly(N- isopropyl acrylamide) (NIP AM).

[0271] In embodiments the cell is lysed to release nucleic acid or other materials from the cells. For example, the cells may be lysed using reagents (e.g., a surfactant such as Triton-X or SDS, an enzyme such as lysozyme, lysostaphin, zymolase, cellulase, mutanolysin, glycanases, proteases, mannase, proteinase K, etc.) or a physical lysing mechanism a physical condition (e.g., ultrasound, ultraviolet light, mechanical agitation, etc.). The cells may release, for instance, DNA, RNA, mRNA, proteins, or enzymes. The cells may arise from any suitable source. For instance, the cells may be any cells for which nucleic acid from the cells is desired to be studied or sequenced, etc., and may include one, or more than one, cell type. The cells may be for example, from a specific population of cells, such as from a certain organ or tissue (e.g., cardiac cells, immune cells, muscle cells, cancer cells, etc.), cells from a specific individual or species (e.g., human cells, mouse cells, bacteria, etc.), cells from different organisms, cells from a naturally- occurring sample (e.g., pond water, soil, etc.), or the like. In some cases, the cells may be dissociated from tissue. In embodiments, the method does not include dissociating the cell from the tissue or the cellular microenvironment. In embodiments, the method does not include lysing the cell.

[0272] In embodiments, the method further includes subjecting the cell to expansion microscopy methods and techniques. Expansion allows individual targets (e.g., mRNA or RNA transcripts) which are densely packed within a cell, to be resolved spatially in a high-throughput manner. Expansion microscopy techniques are known in the art and can be performed as described in US 2016/0116384 and Chen et al., Science, 347, 543 (2015), each of which are incorporated herein by reference in their entirety.

[0273] In embodiments, the method does not include subjecting the cell to expansion microscopy. Typically, expansion microscopy techniques utilize a swellable polymer or hydrogel (e.g., a synthetic matrix-forming material) which can significantly slow diffusion of enzymes and nucleotides. Matrix (e.g., synthetic matrix) forming materials include polyacrylamide, cellulose, alginate, polyamide, cross-linked agarose, cross-linked dextran or cross-linked polyethylene glycol. The matrix forming materials can form a matrix by polymerization and/or crosslinking of the matrix forming materials using methods specific for the matrix forming materials and methods, reagents and conditions known to those of skill in the art. Additionally, expansion microscopy techniques may render the temperature of the cell sample difficult to modulate in a uniform, controlled manner. Modulating temperature provides a useful parameter to optimize amplification and sequencing methods. In embodiments, the method does not include an exogenous matrix.

[0274] In embodiments, the oligonucleotide contains one or more functional moieties (e.g., bioconjugate reactive groups) that serve as attachment points to the cell (i.e., the internal cellular scaffold) or to the matrix in which the cell is embedded (e.g. a hydrogel). In embodiments, the circularizable oligonucleotide contains one or more functional moieties (e.g., bioconjugate reactive groups) that serve as attachment points to the cell (i.e., the internal cellular scaffold) or to the matrix in which the cell is embedded (e.g. a hydrogel). In embodiments, the bioconjugate reactive group is located at the 5’ and/or 3’ end of the oligonucleotide. In embodiments, the bioconjugate reactive group is located at an internal position of the oligonucleotide e.g., the oligonucleotide contains one or more modified nucleotides, such as aminoallyl deoxyuridine 5'- triphosphate (dUTP) nucleotide(s). In embodiments, the functional moiety can be covalently cross-linked, copolymerize with or otherwise non-covalently bound to the matrix. In embodiments, the functional moiety can react with a cross-linker. In embodiments, the functional moiety can be part of a ligand-ligand binding pair. Suitable exemplary functional moieties include an amine, acrydite, alkyne, biotin, azide, and thiol. In embodiments of crosslinking, the functional moiety is cross-linked to modified dNTP or dUTP or both. In embodiments, suitable exemplary cross-linker reactive groups include imidoester (DMP), succinimide ester (NHS), maleimide (Sulfo-SMCC), carbodiimide (DCC, EDC) and phenyl azide. Cross-linkers within the scope of the present disclosure may include a spacer moiety. In embodiments, such spacer moieties may be functionalized. In embodiments, such spacer moieties may be chemically stable. In embodiments, such spacer moieties may be of sufficient length to allow amplification of the nucleic acid bound to the matrix. In embodiments, suitable exemplary spacer moieties include polyethylene glycol, carbon spacers, photo-cleavable spacers and other spacers known to those of skill in the art and the like. In embodiments, the oligonucleotide primer contains a modified nucleotide (e.g., aminoallyl dUTP, 5-TCO-PEG4-dUTP, C8-Alkyne-dUTP, 5-Azidomethyl- dUTP, 5-Vinyl-dUTP, or 5- Ethynyl dLTTP). For example, prior to amplification, the modified nucleotide-containing primer is attached to the cell protein matrix by using a cross-linking reagent (e.g., an amine-reactive crosslinking agent with PEG spacers, such as (PEGylated bis(sulfosuccinimidyl)suberate) (BS(PEG)9)). [0275] In embodiments, the target polynucleotide includes DNA nucleic acid sequences. In embodiments, the target polynucleotide is a cDNA target polynucleotide and before step a), an RNA nucleic acid sequence is reverse transcribed to generate the cDNA target polynucleotide. In embodiments, the target polynucleotide includes an endogenous sequence (e.g., genomic nucleic acid sequences present within the cell).

[0276] In embodiments, ligating includes enzymatic ligation including a ligation enzyme (e.g., Circligase enzyme, Taq DNA Ligase, HiFi Taq DNA Ligase, T4 ligase, PBCV-1 DNA Ligase (also known as SplintR ligase) or Ampligase DNA Ligase). Non-limiting examples of ligases include DNA ligases such as DNA Ligase I, DNA Ligase II, DNA Ligase III, DNA Ligase IV, T4 DNA ligase, T7 DNA ligase, T3 DNA Ligase, E. coli DNA Ligase, PBCV-1 DNA Ligase (also known as SplintR ligase) or a Taq DNA Ligase. In embodiments, the ligase enzyme includes a T4 DNA ligase, T4 RNA ligase 1, T4 RNA ligase 2, T3 DNA ligase or T7 DNA ligase. In embodiments, the enzymatic ligation is performed by a mixture of ligases. In embodiments, the ligation enzyme is selected from the group consisting of T4 DNA ligase, T4 RNA ligase 1, T4 RNA ligase 2, RtcB ligase, T3 DNA ligase, T7 DNA ligase, Taq DNA ligase, PBCV-1 DNA Ligase, a thermostable DNA ligase (e.g., 5’ AppDNA/RNA ligase), an ATP dependent DNA ligase, an RNA-dependent DNA ligase (e.g., SplintR ligase), and combinations thereof. In embodiments, enzymatic ligation includes two different ligation enzymes (e.g., SplintR ligation and T4 DNA ligase, or SplintR ligase and Taq DNA ligase). In embodiments, enzymatic ligation includes more than two different ligation enzymes.

[0277] In embodiments, each oligonucleotide includes a blocking moiety at a 3’ end (e.g., at the 3’ end of each oligonucleotide of a plurality of oligonucleotides). In embodiments, the blocking moiety is reversible. In embodiments, the blocking moiety is irreversible. In embodiments, the blocking moiety at the 3’ end (e.g., the 3’ blocking moiety) includes a reversible terminator. In embodiments, the 3’ blocking moiety includes a dideoxynucleotide triphosphate (e.g., a ddNTP).

[0278] In embodiments, the amplification primer and the sequencing primer includes an oligonucleotide, either natural or synthetic, that is capable, upon forming a duplex with a polynucleotide template, of acting as a point of initiation of nucleic acid synthesis and being extended from its 3’ end along the template so that an extended duplex is formed. The sequence of nucleotides added during the extension process is determined by the sequence of the template polynucleotide. Primers (e.g., amplification primer or sequencing primer) include nucleotides ranging from 17 to 30 nucleotides. In embodiments, the primer is at least 17 nucleotides, or alternatively, at least 18 nucleotides, or alternatively, at least 19 nucleotides, or alternatively, at least 20 nucleotides, or alternatively, at least 21 nucleotides, or alternatively, at least 22 nucleotides, or alternatively, at least 23 nucleotides, or alternatively, at least 24 nucleotides, or alternatively, at least 25 nucleotides, or alternatively, at least 26 nucleotides, or alternatively, at least 27 nucleotides, or alternatively, at least 28 nucleotides, or alternatively, at least 29 nucleotides, or alternatively, at least 30 nucleotides, or alternatively at least 50 nucleotides, or alternatively at least 75 nucleotides or alternatively at least 100 nucleotides. In embodiments, one or more nucleotides within the amplification primer sequence, the sequencing primer sequence, and/or the immobilized oligonucleotide contains one or more functional moieties (e.g., bioconjugate reactive groups) that serve as attachment points to the cell (e.g., to an internal cellular component, such as a protein) or the matrix in which the cell is embedded (e.g. a hydrogel). In embodiments, one or more nucleotides within the amplification primer sequence, the sequencing primer sequence, and/or the first and/or second immobilized oligonucleotide primer contains one or more functional moieties (e.g., bioconjugate reactive groups) that serve as attachment points to complementary bioconjugate reactive groups within the cell (e.g., a protein). In embodiments, a plurality of oligonucleotide primers are provided to the matrix in which the cell is embedded prior to amplification. In embodiments, a plurality of oligonucleotide primers are provided to the matrix in which the cell is embedded concurrently with amplification. In embodiments, the bioconjugate reactive group is located at the 5’ or 3’ end of the primer. In embodiments, the bioconjugate reactive group is located at an internal position of the primer e.g., the primer contains one or more modified nucleotides, such as aminoallyl deoxyuridine 5'- triphosphate (dUTP) nucleotide(s). In embodiments, the functional moiety can be covalently cross-linked, copolymerize with or otherwise non-covalently bound to the matrix. In embodiments, the functional moiety can react with a cross-linker. In embodiments, the functional moiety can be part of a ligand-ligand binding pair. Suitable exemplary functional moieties include an amine, acrydite, alkyne, biotin, azide, and thiol. In embodiments of crosslinking, the functional moiety is cross-linked to modified dNTP or dUTP or both. In embodiments, suitable exemplary cross-linker reactive groups include imidoester (DMP), succinimide ester (NHS), maleimide (Sulfo-SMCC), carbodiimide (DCC, EDC) and phenyl azide. Cross-linkers within the scope of the present disclosure may include a spacer moiety. In embodiments, such spacer moieties may be functionalized. In embodiments, such spacer moieties may be chemically stable. In embodiments, such spacer moieties may be of sufficient length to allow amplification of the nucleic acid bound to the matrix. In embodiments, suitable exemplary spacer moieties include polyethylene glycol, carbon spacers, photo-cleavable spacers and other spacers known to those of skill in the art and the like. In embodiments, the amplification primer and/or the sequencing primer contains a modified nucleotide (e.g., amino-allyl dUTP, 5-TCO-PEG4-dUTP, C8-Alkyne-dUTP, 5- Azidomethyl- dUTP, 5-Vinyl-dUTP, or 5-Ethynyl dLTTP). For example, prior to amplification, the modified nucleotide-containing primer is attached to the cell protein matrix by using a crosslinking reagent (e.g., an amine-reactive crosslinking agent with PEG spacers, such as (PEGylated bis(sulfosuccinimidyl)suberate) (BS(PEG)9)).

[0279] In embodiments, the method includes amplifying the circular polynucleotide by extending an amplification primer with a strand-displacing polymerase, wherein the primer extension generates an extension product including multiple complements of the circular polynucleotide. In embodiments, the method of amplifying includes an isothermal amplification method. In embodiments, the method of amplifying includes rolling circle amplification (RCA) or rolling circle transcription (RCT). In embodiments, the method of amplifying is rolling circle amplification (RCA). In embodiments, amplifying includes exponential rolling circle amplification (eRCA). Exponential RCA is similar to the linear process except that it uses a second primer (e.g., one or more immobilized oligonucleotide(s)) having a sequence that is identical to at least a portion of the circular template (Lizardi et al. Nat. Genet. 19:225 (1998)). This two-primer system achieves isothermal, exponential amplification. Exponential RCA has been applied to the amplification of non-circular DNA through the use of a linear probe that binds at both of its ends to contiguous regions of a target DNA followed by circularization using DNA ligase (Nilsson et al. Science 265(5181):208 5(1994)).

[0280] In embodiments, amplifying the circular oligonucleotide includes incubation with a strand-displacing polymerase. In embodiments, amplifying includes incubation with a stranddisplacing polymerase for about 10 seconds to about 60 minutes. In embodiments, amplifying includes incubation with a strand-displacing polymerase for about 60 seconds to about 60 minutes. In embodiments, amplifying includes incubation with a strand-displacing polymerase for about 10 minutes to about 60 minutes. In embodiments, amplifying includes incubation with a strand-displacing polymerase for about 10 minutes to about 30 minutes. In embodiments, amplifying includes incubation with a strand-displacing polymerase at a temperature of about 20°C to about 50°C. In embodiments, incubation with the strand-displacing polymerase is at a temperature of about 35°C to 42°C. In embodiments, the strand-displacing polymerase is phi29 polymerase, SD polymerase, Bst large fragment polymerase, phi29 mutant polymerase, or a thermostable phi29 mutant polymerase.

[0281] In embodiments, the amplification primer is attached to the solid surface. In embodiments, the amplification primer is in solution. In embodiments, the amplification primer includes one or more phosphorothioate nucleotides. In embodiments, the amplification primer includes a plurality of phosphorothioate nucleotides. In embodiments, about or at least about 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or about 100% of the nucleotides in the amplification primer are phosphorothioate nucleotides. In embodiments, most of the nucleotides in the amplification primer are phosphorothioate nucleotides. In embodiments, all of the nucleotides in the amplification primer are phosphorothioate nucleotides.

[0282] Amplification primer molecules can be fixed to surface by a variety of techniques, including covalent attachment and non-covalent attachment. In embodiments, the amplification primers are confined to an area of a discrete region (referred to as a cluster). The discrete regions may have defined locations in a regular array, which may correspond to a rectilinear pattern, circular pattern, hexagonal pattern, or the like. A regular array of such regions is advantageous for detection and data analysis of signals collected from the arrays during an analysis. These discrete regions are separated by interstitial regions. As used herein, the term “interstitial region” refers to an area in a substrate or on a surface that separates other areas of the substrate or surface. For example, an interstitial region can separate one concave feature of an array from another concave feature of the array. The two regions that are separated from each other can be discrete, lacking contact with each other. In another example, an interstitial region can separate a first portion of a feature from a second portion of a feature. In embodiments the interstitial region is continuous whereas the features are discrete, for example, as is the case for an array of wells in an otherwise continuous surface. The separation provided by an interstitial region can be partial or full separation. Interstitial regions will typically have a surface material that differs from the surface material of the features on the surface. For example, features of an array can have primers that exceeds the amount or concentration present at the interstitial regions. In some embodiments the primers may not be present at the interstitial regions. In embodiments, the amplification primer is attached to a solid support and a template polynucleotide is hybridized to the primer. In embodiments, at least two different primers are attached to the solid support (e.g., a forward and a reverse primer), which facilitates generating multiple amplification products from the first extension product or a complement thereof.

[0283] In embodiments, the extension product includes three or more copies of the target nucleic acid (e.g., the barcode sequence). In embodiments, the extension product includes at least three or more copies of the target nucleic acid. In embodiments, the extension product includes at least five or more copies of the target nucleic acid. In embodiments, the extension product includes at 5 to 10 copies of the target nucleic acid. In embodiments, the extension product includes 10 to 20 copies of the target nucleic acid. In embodiments, the extension product includes 20 to 50 copies of the target nucleic acid. [0284] In embodiments, the oligonucleotide is covalently attached to the matrix or to a cellular component via a bioconjugate reactive linker. In embodiments, the 5' end of the oligonucleotide contains a functional group that is capable of reacting with a complementary group so the primer may be tethered to a cellular component (e.g., a protein). In embodiments, the 3' end of the oligonucleotide contains a functional group that is capable of reacting with a complementary group so the primer may be tethered to a cellular component (e.g., a protein). Non-limiting examples of covalent attachment include amine-modified polynucleotides within the oligonucleotide reacting with epoxy or isothiocyanate groups within the matrix, succinylated polynucleotides within the oligonucleotide reacting with aminophenyl or aminopropyl functional groups within the matrix, dibenzocycloctyne-modified polynucleotides within the oligonucleotide reacting with azide functional groups within the matrix (or vice versa), trans-cyclooctyne- modified polynucleotides within the oligonucleotide reacting with tetrazine or methyl tetrazine groups within the matrix (or vice versa), disulfide modified polynucleotides within the oligonucleotide reacting with mercapto-functional groups within the matrix, amine-functionalized polynucleotides within the oligonucleotide reacting with carboxylic acid groups within the matrix or cellular component via l-ethyl-3-(3-dimethylaminopropyl)-carbodiimide hydrochloride (EDC) chemistry, thiol-modified polynucleotides within the oligonucleotide attaching to the matrix or cellular component via a disulfide bond or maleimide linkage, alkyne-modified polynucleotides within the oligonucleotide attaching to a matrix via copper-catalyzed click reactions to azide functional groups within the matrix, azide-modified polynucleotides within the oligonucleotide attaching to the matrix via copper-catalyzed click reactions to alkyne functional groups within the matrix, and acrydite-modified polynucleotides within the oligonucleotide polymerizing with free acrylic acid monomers within the matrix to form polyacrylamide. In embodiments, the oligonucleotide is attached to the matrix through electrostatic binding. For example, the negatively charged phosphate backbone of the oligonucleotide may be bound electrostatically to positively charged monomers in the solid support.

[0285] In embodiments, the oligonucleotide includes a first bioconjugate reactive group. In embodiments, the oligonucleotide is attached to a cellular compartment. In embodiments, the cellular component includes a second bioconjugate reactive group. In embodiments, the first bioconjugate reactive group is attached to the second bioconjugate reactive group by covalent or non-covalent bonding. In embodiments, the oligonucleotide is covalently attached to a cellular component. In embodiments, the 5' end of the oligonucleotide contains a functional group that is tethered to the cellular component. In embodiments, the oligonucleotide is covalently attached to a matrix within the cell. In embodiments, the 5' end of the oligonucleotide contains a functional group that is tethered to the matrix within the cell. Non-limiting examples of covalent attachment include amine-modified polynucleotides reacting with epoxy or isothiocyanate groups in the cell or matrix within the cell, succinylated polynucleotides reacting with aminophenyl or aminopropyl functional groups in the cell or matrix within the cell, dibenzocycloctyne-modified polynucleotides reacting with azide functional groups in the cell or matrix within the cell (or vice versa), trans-cyclooctyne-modified polynucleotides reacting with tetrazine or methyl tetrazine groups in the cell or matrix within the cell (or vice versa), disulfide modified polynucleotides reacting with mercapto-functional groups in the cell or matrix within the cell, amine- functionalized polynucleotides reacting with carboxylic acid groups in the cell or matrix within the cell via l-ethyl-3-(3-dimethylaminopropyl)-carbodiimide hydrochloride (EDC) chemistry, thiol-modified polynucleotides attaching to cell or matrix within the cell via a disulphide bond or maleimide linkage, alkyne-modified polynucleotides attaching to the cell or matrix within the cell via copper-catalyzed click reactions to azide functional groups in the cell or matrix within the cell, and acrydite-modified polynucleotides polymerizing with free acrylic acid monomers in the cell or matrix within the cell to form polyacrylamide or reacting with thiol groups in the cell or matrix within the cell. In embodiments, the oligonucleotide is attached to the polymer through electrostatic binding. For example, the negatively charged phosphate backbone of the oligonucleotide may be bound electrostatically to positively charged monomers in the matrix.

[0286] In embodiments, the oligonucleotide, or splint oligonucleotide, is attached to the matrix or to a cellular component via a specific binding reagent. In embodiments, the specific binding reagent includes an antibody, single-chain Fv fragment (scFv), antibody fragment-antigen binding (Fab), or an aptamer. In embodiments, the specific binding reagent includes an antibody, or antigen binding fragment, an aptamer, affimer, or non-immunoglobulin scaffold. In embodiments, the specific binding reagent is a peptide, a cell penetrating peptide, an aptamer, a DNA aptamer, an RNA aptamer, an antibody, an antibody fragment, a light chain antibody fragment, a singlechain variable fragment (scFv), a lipid, a lipid derivative, a phospholipid, a fatty acid, a triglyceride, a glycerolipid, a glycerophospholipid, a sphingolipid, a saccharolipid, a polyketide, a polylysine, polyethyleneimine, diethylaminoethyl (DEAE)-dextran, cholesterol, or a sterol moiety. For example, the matrix or cellular component (e.g., a protein) may contain a complementary specific binding reagent to the oligonucleotide containing a specific binding reagent.

[0287] In embodiments, the method further includes detecting the amplification product. In embodiments, detecting the amplification product includes hybridizing an oligonucleotide associated with a detectable label to the amplification product and identifying the detectable label. In embodiments, detecting includes two-dimensional (2D) or three-dimensional (3D) fluorescent microscopy. Suitable imaging technologies are known in the art, as exemplified by Larsson et al., Nat. Methods (2010) 7:395-397 and associated supplemental materials, the entire content of which is incorporated by reference herein in its entirety. In embodiments of the methods provided herein, the imaging is accomplished by confocal microscopy. Confocal fluorescence microscopy involves scanning a focused laser beam across the sample, and imaging the emission from the focal point through an appropriately-sized pinhole. This suppresses the unwanted fluorescence from sections at other depths in the sample. In embodiments, the imaging is accomplished by multi-photon microscopy (e.g., two-photon excited fluorescence or two-photon-pumped microscopy). Unlike conventional single-photon emission, multi-photon microscopy can utilize much longer excitation wavelength up to the red or near-infrared spectral region. This lower energy excitation requirement enables the implementation of semiconductor diode lasers as pump sources to significantly enhance the photostability of materials. Scanning a single focal point across the field of view is likely to be too slow for many sequencing applications. To speed up the image acquisition, an array of multiple focal points can be used. The emission from each of these focal points can be imaged onto a detector, and the time information from the scanning mirrors can be translated into image coordinates. Alternatively, the multiple focal points can be used just for the purpose of confining the fluorescence to a narrow axial section, and the emission can be imaged onto an imaging detector, such as a CCD, EMCCD, or s-CMOS detector. A scientific grade CMOS detector offers an optimal combination of sensitivity, readout speed, and low cost. One configuration used for confocal microscopy is spinning disk confocal microscopy. In 2-photon microscopy, the technique of using multiple focal points simultaneously to parallelize the readout has been called Multifocal Two-Photon Microscopy (MTPM). Several techniques for MTPM are available, with applications typically involving imaging in biological tissue. In embodiments of the methods provided herein, the imaging is accomplished by light sheet fluorescence microscopy (LSFM). In embodiments, detecting includes 3D structured illumination (3DSIM). In 3DSIM, patterned light is used for excitation, and fringes in the Moire pattern generated by interference of the illumination pattern and the sample, are used to reconstruct the source of light in three dimensions. In order to illuminate the entire field, multiple spatial patterns are used to excite the same physical area, which are then digitally processed to reconstruct the final image. See York, Andrew G., et al. “Instant super-resolution imaging in live cells and embryos via analog image processing.” Nature methods 10.11 (2013): 1122-1126 which is incorporated herein by reference. In embodiments, detecting includes selective planar illumination microscopy, light sheet microscopy, emission manipulation, pinhole confocal microscopy, aperture correlation confocal microscopy, volumetric reconstruction from slices, deconvolution microscopy, or aberration-corrected multifocus microscopy. In embodiments, detecting includes digital holographic microscopy (see for example Manoharan, V. N. Frontiers of Engineering: Reports on Leading-edge Engineering from the 2009 Symposium, 2010, 5-12, which is incorporated herein by reference). In embodiments, detecting includes confocal microscopy, light sheet microscopy, or multi-photon microscopy.

[0288] In embodiments, the method further includes sequencing the amplification product. In embodiments, sequencing includes sequencing by synthesis, sequencing by binding, sequencing by ligation, or pyrosequencing. In embodiments, sequencing includes extending a sequencing primer by incorporating a labeled nucleotide or labeled nucleotide analogue, and detecting the label to generate a signal for each incorporated nucleotide or nucleotide analogue, wherein the sequencing primer is hybridized to the extension product. In embodiments, the sequencing primer includes a sequence of the subject sequence.

[0289] In embodiments, the method includes sequencing the amplification products, which includes the barcode sequence. A variety of sequencing methodologies can be used such as sequencing-by synthesis (SBS), pyrosequencing, sequencing by ligation (SBL), or sequencing by hybridization (SBH). Pyrosequencing detects the release of inorganic pyrophosphate (PPi) as particular nucleotides are incorporated into a nascent nucleic acid strand (Ronaghi, et al., Analytical Biochemistry 242(1), 84-9 (1996); Ronaghi, Genome Res. 11(1), 3-11 (2001); Ronaghi et al. Science 281(5375), 363 (1998); U.S. Pat. Nos. 6,210,891; 6,258,568; and. 6,274,320, each of which is incorporated herein by reference in its entirety). In pyrosequencing, released PPi can be detected by being converted to adenosine triphosphate (ATP) by ATP sulfurylase, and the level of ATP generated can be detected via light produced by luciferase. In this manner, the sequencing reaction can be monitored via a luminescence detection system. In both SBL and SBH methods, target nucleic acids, and amplicons thereof, are subjected to repeated cycles of oligonucleotide delivery and detection. SBL methods, include those described in Shendure et al. Science 309: 1728-1732 (2005); U.S. Pat. Nos. 5,599,675; and 5,750,341, each of which is incorporated herein by reference in its entirety; and the SBH methodologies are as described in Bains et al., Journal of Theoretical Biology 135(3), 303-7 (1988); Drmanac et al., Nature Biotechnology 16, 54-58 (1998); Fodor et al., Science 251(4995), 767-773 (1995); and WO 1989/10977, each of which is incorporated herein by reference in its entirety.

[0290] In SBS, extension of a nucleic acid primer along a nucleic acid template is monitored to determine the sequence of nucleotides in the template. The underlying chemical process can be catalyzed by a polymerase, wherein fluorescently labeled nucleotides are added to a primer (thereby extending the primer) in a template dependent fashion such that detection of the order and type of nucleotides added to the primer can be used to determine the sequence of the template. In embodiments, sequencing includes annealing and extending a sequencing primer to incorporate a detectable label that indicates the identity of a nucleotide in the target polynucleotide, detecting the detectable label, and repeating the extending and detecting of steps. In embodiments, the methods include sequencing one or more bases of a target nucleic acid by extending a sequencing primer hybridized to a target nucleic acid (e.g., an amplification product produced by the amplification methods described herein). In embodiments, sequencing may be accomplished by a sequencing-by-synthesis (SBS) process. In embodiments, sequencing includes a sequencing by synthesis process, where individual nucleotides are identified iteratively, as they are polymerized to form a growing complementary strand. In embodiments, nucleotides added to a growing complementary strand include both a label and a reversible chain terminator that prevents further extension, such that the nucleotide may be identified by the label before removing the terminator to add and identify a further nucleotide. Such reversible chain terminators include removable 3’ blocking groups, for example as described in U.S. Pat. Nos. 7,541,444 and 7,057,026. Once such a modified nucleotide has been incorporated into the growing polynucleotide chain complementary to the region of the template being sequenced, there is no free 3'-OH group available to direct further sequence extension and therefore the polymerase cannot add further nucleotides. Once the identity of the base incorporated into the growing chain has been determined, the 3’ reversible terminator may be removed to allow addition of the next successive nucleotide. By ordering the products derived using these modified nucleotides it is possible to deduce the DNA sequence of the oligonucleotide target nucleic acid sequence.

[0291] In embodiments, the methods of sequencing a nucleic acid include a extending a polynucleotide by using a polymerase. In embodiments, the polymerase is a DNA polymerase. In embodiments, the DNA polymerase is a Pol I DNA polymerase, Pol II DNA polymerase, Pol III DNA polymerase, Pol IV DNA polymerase, Pol V DNA polymerase, Pol P DNA polymerase, Pol p DNA polymerase, Pol X DNA polymerase, Pol c DNA polymerase, Pol a DNA polymerase, Pol 5 DNA polymerase, Pol a DNA polymerase, Pol q DNA polymerase, Pol r DNA polymerase, Pol K DNA polymerase, Pol C, DNA polymerase, Pol y DNA polymerase, Pol 9 DNA polymerase, Pol u DNA polymerase, or a thermophilic nucleic acid polymerase (e.g., Therminator y, 9°N polymerase (exo-), Therminator II, Therminator III, or Therminator IX). In embodiments, the DNA polymerase is a thermophilic nucleic acid polymerase. In embodiments, the DNA polymerase is a modified archaeal DNA polymerase. In embodiments, the polymerase is a mutant P. abyssi polymerase (e.g., such as a mutant P. abyssi polymerase described in WO 2018/148723 or WO 2020/056044, each of which are incorporated herein by reference for all purposes). In embodiments, the polymerase is a bacterial DNA polymerase, eukaryotic DNA polymerase, archaeal DNA polymerase, viral DNA polymerase, or phage DNA polymerases. Bacterial DNA polymerases include E. coli DNA polymerases I, II and III, IV and V, the KI enow fragment of E. coli DNA polymerase, Clostridium stercorarium (Cst) DNA polymerase, Clostridium thermocellum (Cth) DNA polymerase and Sulfolobus solfataricus (Sso) DNA polymerase. Eukaryotic DNA polymerases include DNA polymerases a, P, y, 5, €, r], , c, p, and k, as well as the Revl polymerase (terminal deoxycytidyl transferase) and terminal deoxynucleotidyl transferase (TdT). Viral DNA polymerases include T4 DNA polymerase, phi-29 DNA polymerase, GA-1, phi-29-like DNA polymerases, PZA DNA polymerase, phi- 15 DNA polymerase, Cpl DNA polymerase, Cpl DNA polymerase, T7 DNA polymerase, and T4 polymerase. Other useful DNA polymerases include thermostable and/or thermophilic DNA polymerases such as Thermus aquaticus (Taq) DNA polymerase, Thermus filiformis (Tfi) DNA polymerase, Thermococcus zilligi (Tzi) DNA polymerase, Thermus thermophilus (Tth) DNA polymerase, Thermus flavusu (Tfl) DNA polymerase, Pyrococcus woesei (Pwo) DNA polymerase, Pyrococcus furiosus (Pfu) DNA polymerase and Turbo Pfu DNA polymerase, Thermococcus litoralis (Tli) DNA polymerase, Pyrococcus sp. GB-D polymerase, Thermotoga maritima (Tma) DNA polymerase, Bacillus stearothermophilus (Bst) DNA polymerase, Pyrococcus Kodakaraensis (KOD) DNA polymerase, Pfx DNA polymerase, Thermococcus sp. JDF-3 (JDF-3) DNA polymerase, Thermococcus gorgonarius (Tgo) DNA polymerase, Thermococcus acidophilium DNA polymerase; Sulfolobus acidocaldarius DNA polymerase; Thermococcus sp. go N-7 DNA polymerase; Pyrodictium occultum DNA polymerase; Methanococcus voltae DNA polymerase; Methanococcus thermoautotrophicum DNA polymerase; Methanococcus jannaschii DNA polymerase; Desulfurococcus strain TOK DNA polymerase (D. Tok Pol); Pyrococcus abyssi DNA polymerase; Pyrococcus horikoshii DNA polymerase; Pyrococcus islandicum DNA polymerase; Thermococcus fumicolans DNA polymerase; Aeropyrum pernix DNA polymerase; and the heterodimeric DNA polymerase DP1/DP2. In embodiments, the polymerase is 3PDX polymerase as disclosed in U.S. 8,703,461, the disclosure of which is incorporated herein by reference. In embodiments, the polymerase is a reverse transcriptase. Exemplary reverse transcriptases include, but are not limited to, HIV-1 reverse transcriptase from human immunodeficiency virus type 1 (PDB 1HMV), HIV-2 reverse transcriptase from human immunodeficiency virus type 2, M-MLV reverse transcriptase from the Moloney murine leukemia virus, AMV reverse transcriptase from the avian myeloblastosis virus, and Telomerase reverse transcriptase. [0292] In embodiments, sequencing includes a plurality of sequencing cycles. In embodiments, sequencing includes 20 to 100 sequencing cycles. In embodiments, sequencing includes 50 to 100 sequencing cycles. In embodiments, sequencing includes 50 to 300 sequencing cycles. In embodiments, sequencing includes 50 to 150 sequencing cycles. In embodiments, sequencing includes at least 10, 20, 30 40, or 50 sequencing cycles. In embodiments, sequencing includes at least 10 sequencing cycles. In embodiments, sequencing includes 10 to 20 sequencing cycles. In embodiments, sequencing includes 10, 11, 12, 13, 14, or 15 sequencing cycles. In embodiments, sequencing includes (a) extending a sequencing primer by incorporating a labeled nucleotide, or labeled nucleotide analogue and (b) detecting the label to generate a signal for each incorporated nucleotide or nucleotide analogue.

[0293] In embodiments, sequencing includes sequentially extending a plurality of sequencing primers (e.g., sequencing a first region of a target nucleic acid followed by sequencing a second region of a target nucleic acid, followed by sequencing N regions, where is the number of sequencing primers in the known sequencing primer set). In embodiments, sequencing includes generating a plurality of sequencing reads.

[0294] In embodiments, sequencing includes extending a sequencing primer to generate a sequencing read. In embodiments, sequencing includes extending a sequencing primer by incorporating a labeled nucleotide, or labeled nucleotide analogue and detecting the label to generate a signal for each incorporated nucleotide or nucleotide analogue. In embodiments, the labeled nucleotide or labeled nucleotide analogue further includes a reversible terminator moiety. In embodiments, the labeled nucleotide or labeled nucleotide analogue further includes a reversible terminator moiety. In embodiments, the reversible terminator moiety is attached to the

, wherein the 3’ oxygen is explicitly depicted in the above formulae. Additional examples of reversible terminators may be found in U.S. Patent No. 6,664,079, Ju J. et al. (2006) Proc Natl Acad Sci USA 103(52): 19635-19640.; Ruparel H. et al. (2005) Proc Natl Acad Set USA 102(17):5932-5937.; Wu J. et al. (2007) Proc Natl Acad Sci USA 104(104): 16462-16467; Guo J. et al. (2008) Proc Natl Acad Sci USA 105(27): 9145-9150 Bentley D. R. et al. (2008) Nature 456(7218):53-59; or Hutter D. et al. (2010) Nucleosides Nucleotides & Nucleic Acids 29 :879-895, which are incorporated herein by reference in their entirety for all purposes. In embodiments, a polymerase-compatible cleavable moiety includes an azido moiety or a dithiol moiety.

[0295] In embodiments, the method includes sequencing a plurality of target polynucleotides of a cell in situ within an optically resolved volume. In embodiments, the number of unique targets detected within an optically resolved volume of a sample is about 3, 10, 30, 50, or 100. In embodiments, the number of unique targets detected within an optically resolved volume of a sample is about 1 to 10. In embodiments, the number of unique targets detected within an optically resolved volume of a sample is about 5 to 10. In embodiments, the number of unique targets detected within an optically resolved volume of a sample is about 1 to 5. In embodiments, the number of unique targets detected within an optically resolved volume of a sample is at least 3, 10, 30, 50, or 100. In embodiments, the number of unique targets detected within an optically resolved volume of a sample is less than 3, 10, 30, 50, or 100. In embodiments, the number of unique targets detected within an optically resolved volume of a sample is about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, 100, 500, 1,000, 5,000, 10,000, or 200,000. In embodiments, the methods allow for detection of a single target of interest. In embodiments, the methods allow for multiplex detection of a plurality of targets of interest.

[0296] In embodiments, the optically resolved volume has an axial resolution (i.e., depth, or z) that is greater than the lateral resolution (i.e., xy plane). In embodiments, the optically resolved volume has an axial resolution that is greater than twice the lateral resolution. In embodiments, the dimensions (i.e., the x, y, and z dimensions) of the optically resolved volume are about 0.5 pm x 0.5 pm x 0.5 pm; 1 pm x 1 pm x 1 pm; 2 pm x 2 pm x 2 pm; 0.5 pm x 0.5 pm x 1 pm; 0.5 pm x 0.5 pm x 2 pm; 2 pm x 2 pm x 1 pm; or 1 pm x 1 pm x 2 pm. In embodiments, the dimensions (i.e., the x, y, and z dimensions) of the optically resolved volume are about 1 pm x 1 pm x 2 pm; 1 pm x 1 pm x 3 pm; 1 pm x 1 pm x 4 pm; or about 1 pm x 1 pm x 5 pm. See FIG. 5, for example. In embodiments, the dimensions (i.e., the x, y, and z dimensions) of the optically resolved volume are about 1 pm x 1 pm x 5 pm. In embodiments, the dimensions (i.e., the x, y, and z dimensions) of the optically resolved volume are about 1 pm x 1 pm x 6 pm. In embodiments, the dimensions (i.e., the x, y, and z dimensions) of the optically resolved volume are about 1 pm x 1 pm x 7 pm. In embodiments, the optically resolved volume is a cubic micron. In embodiments, the optically resolved volume has a lateral resolution from about 100 to 200 nanometers, from 200 to 300 nanometers, from 300 to 400 nanometers, from 400 to 500 nanometers, from 500 to 600 nanometers, or from 600 to 1000 nanometers. In embodiments, the optically resolved volume has a axial resolution from about 100 to 200 nanometers, from 200 to 300 nanometers, from 300 to 400 nanometers, from 400 to 500 nanometers, from 500 to 600 nanometers, or from 600 to 1000 nanometers. In embodiments, the optically resolved volume has a axial resolution from about 1 to 2 pm, from 2 to 3 pm, from 3 to 4 pm, from 4 to 5 pm, from 5 to 6 pm, or from 6 to 10 pm.

[0297] In embodiments, the method further includes an additional imaging modality, immunofluorescence (IF), or immunohistochemistry modality (e.g., immunostaining). In embodiments, the method includes ER staining (e.g., contacting the cell with a cell-permeable dye which localizes to the endoplasmic reticula), Golgi staining (e.g., contacting the cell with a cell- permeable dye which localizes to the Golgi), F-actin staining (e.g., contacting the cell with a phalloidin-conjugated dye that binds to actin filaments), lysosomal staining (e.g., contacting the cell with a cell-permeable dye that accumulates in the lysosome via the lysosome pH gradient), mitochondrial staining (e.g., contacting the cell with a cell-permeable dye which localizes to the mitochondria), nucleolar staining, or plasma membrane staining. For example, the method includes live cell imaging (e.g., obtaining images of the cell) prior to or during fixing, immobilizing, and permeabilizing the cell. Immunohistochemistry (IHC) is a powerful technique that exploits the specific binding between an antibody and antigen to detect and localize specific antigens in cells and tissue, commonly detected and examined with the light microscope. Known IHC modalities may be used, such as the protocols described in Magaki, S., Hojat, S. A., Wei, B., So, A., & Yong, W. H. (2019). Methods in molecular biology (Clifton, N.J.), 1897, 289-298, which is incorporated herein by reference. In embodiments, the additional imaging modality includes bright field microscopy, phase contrast microscopy, Nomarski differential-interference- contrast microscopy, or dark field microscopy. In embodiments, the method further includes determining the cell morphology (e.g., the cell boundary or cell shape) using known methods in the art. For example, to determining the cell boundary includes comparing the pixel values of an image to a single intensity threshold, which may be determined quickly using histogram-based approaches as described in Carpenter, A. et al Genome Biology 7, R100 (2006) and Arce, S., Sci Rep 3, 2266 (2013)). [0298] In embodiments, the target polynucleotide is in a cell. In embodiments, the oligonucleotide probe and the splint oligonucleotide are in the cell. In embodiments, the cell is permeabilized and immobilized to a solid support surface. In embodiments, the cell is attached to a substrate. In embodiments, the cell is attached to the substrate via a bioconjugate reactive moiety. In embodiments, the composition is within a cell or tissue sample. In embodiments, the cell or tissue sample is cleared (e.g., digested) of proteins, lipids, or proteins and lipids. In embodiments, the cell or tissue sample is processed according to a known technique in the art, for example CLARITY (Chung K., et al. Nature 497, 332-337 (2013)), PACT-PARS (Yang Bet al. Cell 158, 945-958 (2014).), CUBIC (Susaki E. A. et al. Cell 157, 726-739 (2014)., 18), ScaleS (Hama H., et al. Nat. Neurosci. 18, 1518-1529 (2015)), OPTIClear (Lai H. M., et al. Nat. Commun. 9, 1066 (2018)), Ce3D (Li W., et al. Proc. Natl. Acad. Sci. U.S.A. 114, E7321-E7330 (2017)), BABB (Dodt H.U. et al. Nat. Methods 4, 331-336 (2007)), iDISCO (Renier N., et al. Cell 159, 896-910 (2014)), uDISCO (Pan C., et al. Nat. Methods 13, 859-867 (2016)), FluoClearBABB (Schwarz M. K., et al. PLOS ONE 10, e0124650 (2015)), Ethanol-ECi (Klingberg A., et al. J. Am. Soc. Nephrol. 28, 452-459 (2017)), and PEGASOS (Jing D. et al. Cell Res. 28, 803-818 (2018)).

[0299] In embodiments, the barcodes in the known set of barcodes have a specified Hamming distance. In embodiments, the Hamming distance is 4 to 15. In embodiments, the Hamming distance is 8 to 12. In embodiments, the Hamming distance is 10. In embodiments, the Hamming distance is 0 to 100. In embodiments, the Hamming distance is 0 to 15. In embodiments, the Hamming distance is 0 to 10. In embodiments, the Hamming distance is 1 to 10. In embodiments, the Hamming distance is 5 to 10. In embodiments, the Hamming distance is 1 to 100. In embodiments, the Hamming distance between any two barcode sequences of the set is at least 2, 3, 4, or 5. In embodiments, the Hamming distance between any two barcode sequences of the set is at least 3. In embodiments, the Hamming distance between any two barcode sequences of the set is at least 4.

[0300] In embodiments, demultiplexing the multiplexed signal includes a linear decomposition of the multiplexed signal. Any of a variety of techniques may be employed for decomposition of the multiplexed signal. Examples include, but are not limited to, Zimmerman et al. Chapter 5: Clearing Up the Signal: Spectral Imaging and Linear Unmixing in Fluorescence Microscopy; Confocal Microscopy: Methods and Protocols, Methods in Molecular Biology, vol. 1075 (2014); Shirawaka H. et al.; Biophysical Journal Volume 86, Issue 3, March 2004, Pages 1739-1752; and S. Schlachter, et al, Opt. Express 17, 22747-22760 (2009); the content of each of which is incorporated herein by reference in its entirety. In embodiments, multiplexed signal includes overlap of a first signal and a second signal and is computationally resolved, for example, by imaging software.

[0301] In embodiments, the method further includes measuring an amount of one or more of the targets by counting the one or more associated barcodes. In embodiments, the method further includes counting the one or more associated barcodes in an optically resolved volume. In embodiments, the number of unique targets detected within an optically resolved volume of a sample is about 3, 10, 30, 50, or 100. In embodiments, the number of unique targets detected within an optically resolved volume of a sample is about 1 to 10. In embodiments, the number of unique targets detected within an optically resolved volume of a sample is about 5 to 10. In embodiments, the number of unique targets detected within an optically resolved volume of a sample is about 1 to 5. In embodiments, the number of unique targets detected within an optically resolved volume of a sample is at least 3, 10, 30, 50, or 100. In embodiments, the number of unique targets detected within an optically resolved volume of a sample is less than 3, 10, 30, 50, or 100. In embodiments, the number of unique targets detected within an optically resolved volume of a sample is about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, 100, 500, 1,000, 5,000, 10,000, or 200,000. In embodiments, the methods allow for detection of a single target of interest. In embodiments, the methods allow for multiplex detection of a plurality of targets of interest. The use of oligonucleotide barcodes with unique identifier sequences as described herein allows for simultaneous detection of 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1,000, 1,500, 2,000, 2,500, 3,000, 3,500, 4,000, 4,500, 5,000, 5,500, 6,000, 6,500, 7,000, 7,500, 8,000, 8,500, 9,000, 9,500, 10,000 or more than 10,000 unique targets within a single cell. In contrast to existing in situ detection methods, the methods presented herein have the advantage of virtually limitless numbers of individually detected molecules in parallel and in situ.

[0302] In embodiments, the total volume of the cell is about 1 to 25 pm³. In embodiments, the volume of the cell is about 5 to 10 pm³. In embodiments, the volume of the cell is about 3 to 7 pm³.

[0303] In aspects and embodiments described herein, the methods are useful in the field of predictive medicine in which diagnostic assays, prognostic assays, pharmacogenomics, and monitoring clinical trials are used for prognostic (i.e., predictive) purposes to thereby treat an individual prophylactically. Accordingly, in embodiments the methods of diagnosing and/or prognosing one or more diseases and/or disorders using one or more of expression profiling methods described herein are provided. [0304] In an aspect is provided a method of detecting a disorder (e.g., cancer) or a diseasecausing mutation or allele in a cell. In embodiments, the cell includes an oncogene (e.g., HER2, BRAF, EGFR, KRAS) and utilizing the methods described herein the oncogene is identified, thereby detecting a disorder when the presence of the oncogene is identified. In embodiments, the sample includes a nucleic acid molecule which includes a disease-causing mutation or allele. In embodiments, the method includes hybridizing an oligonucleotide primer which is correlated with the disease-causing mutation or allele. In embodiments, the method includes ligating a mutationspecific oligonucleotide only when the disease-causing mutation or allele is present in the nucleic acid target. In embodiments, the disease-causing mutation or allele is a base substitution, an insertion mutation, a deletion mutation, a gene amplification, a gene deletion, a gene fusion event, or a gene inversion event.

[0305] In embodiments, the mutation or allele is associated with an increased predisposition for one or more diseases, disorders, or other phenotypes. In embodiments, the mutation or allele is associated with a decreased predisposition for one or more diseases, disorders, or other phenotypes. For example, some mutations or alleles are associated with a cancer phenotype, such as decreased growth inhibition, evasion of immune detection, or dedifferentiation. Mutations that can be detected using the method provided herein include for example, mutations to BRAF, EGFR, Her2/ERBB2, and other somatic mutations as exemplified by Greenman et al., Nature (2007) 446: 153-158, hereby incorporated by reference in its entirety.

[0306] In embodiments, the method further includes detecting a biomolecule (e.g., a protein) in the cell or tissue. Means for detecting biomolecules are described, for example, in US Patent No. US 11,492,662; US 11,643,679; US 11,434,525; US 11,680,288; and/or US 11,753,678, each of which are incorporated herein in their entirety. In embodiments, detecting the protein includes antibodies specific to the protein of interest, conjugated to enzymes, oligonucleotides or fluorescent dyes. Antibody-oligonucleotide conjugates provide the ability to multiplex and detect multiple proteins. For example, the oligonucleotide provides a sequence that is associated with the antibody, and so when the sequence of the oligonucleotide is inferred or detected the identity of the antibody and thus the target protein of interest is identified. In embodiments, the method includes contacting the cell or tissue with an antibody-oligo (Ab-O) conjugate, wherein the oligonucleotide is covalently attached to the Ab-O. The oligonucleotide may be detected with a circular, or circularizable, probe. A type of circularizable probe is a padlock probe (PLP) which is a linear polynucleotide that is rendered into a circular polynucleotide following hybridization to the oligonucleotide and ligation of the 5’ and 3’ ends. [0307] In embodiments, the biomolecule to be detected in the tissue section or in the cell is contacted with a detection agent. In embodiments, the biomolecule to be detected on the surface of the tissue section or on the surface of a cell is contacted with a detection agent. In embodiments, the detection agent includes a protein-specific binding agent. In embodiments, the detection agent includes a protein-specific binding agent bound to a nucleic acid sequence, bioconjugate reactive moiety, an enzyme, or a fluorophore. In embodiments, the protein-specific binding agent is an antibody, single domain antibody, single-chain Fv fragment (scFv), antibody fragment-antigen binding (Fab), affimer, or an aptamer. In embodiments, the protein-specific binding agent is an antibody. In embodiments, the protein-specific binding agent is a single domain antibody. In embodiments, the protein-specific binding agent is a single-chain Fv fragment (scFv). In embodiments, the protein-specific binding agent is an antibody fragmentantigen binding (Fab). In embodiments, the protein-specific binding agent is an affimer. In embodiments, the protein-specific binding agent is an aptamer.

[0308] In embodiments, the detection agent includes a protein-specific binding agent or oligonucleotide-specific binding agent. In embodiments, the detection agent includes a proteinspecific binding agent. In embodiments, the detection agent includes an oligonucleotide-specific binding agent. In embodiments, the detection agent includes an oligonucleotide-specific binding agent including an identifying nucleic acid sequence. In embodiments, the detection agent includes an oligonucleotide-specific binding agent bound to a bioconjugate reactive moiety, an enzyme, or a fluorophore.

[0309] In an aspect is provided a method of identifying a cell that responds to a genetically modifying agent, the method including administering a genetically modifying agent to the cell, detecting whether an agent-mediated nucleic acid sequence is present in the cell by sequencing a plurality of target nucleic acids according to the methods as described herein, and identifying a cell that responds to a genetically modifying agent when the presence of the agent-mediated nucleic acid is detected in the cell. In embodiments, the method includes contacting a cell or tissue with a probe oligonucleotide and binding an RNA binding sequence of the probe oligonucleotide to an RNA molecule, wherein the probe oligonucleotide further includes a splint binding sequence; extending the RNA binding sequence along the RNA molecule to form a complementary sequence including a first target sequence and a second target sequence; contacting the cell or tissue with a splint oligonucleotide and binding a first sequence of the splint oligonucleotide to the splint binding sequence and binding a second sequence of the splint oligonucleotide to the second target sequence; forming a circular polynucleotide including the first sequence, or a complement thereof, and the second sequence, or a complement thereof; amplifying the circular polynucleotide to generate an amplification product including multiple copies of the first sequence, or a complement thereof, and the second sequence, or a complement thereof; and detecting (e.g., sequencing) the amplification product. In embodiments, the method includes serially cycling through detection cycles to determine the sequence, wherein each detection cycle includes hybridizing, detecting, and removing a fluorescently labelled oligonucleotide.

[0310] In an aspect is provided a method of identifying an agent as a genetically modifying agent, the method including administering an agent to a cell, detecting whether an agent-mediated nucleic acid sequence is present in the cell by sequencing a plurality of target nucleic acids according to any of the methods as described herein, and identifying the genetically modifying agent when the presence of the agent-mediated nucleic acid is detected in the cell. In embodiments, the method includes contacting a cell or tissue with a probe oligonucleotide and binding an RNA binding sequence of the probe oligonucleotide to an RNA molecule, wherein the probe oligonucleotide further includes a splint binding sequence; extending the RNA binding sequence along the RNA molecule to form a complementary sequence including a first target sequence and a second target sequence; contacting the cell or tissue with a splint oligonucleotide and binding a first sequence of the splint oligonucleotide to the splint binding sequence and binding a second sequence of the splint oligonucleotide to the second target sequence; forming a circular polynucleotide including the first sequence, or a complement thereof, and the second sequence, or a complement thereof; amplifying the circular polynucleotide to generate an amplification product including multiple copies of the first sequence, or a complement thereof, and the second sequence, or a complement thereof; and detecting (e.g., sequencing) the amplification product. In embodiments, the method includes serially cycling through detection cycles to determine the sequence, wherein each detection cycle includes hybridizing, detecting, and removing a fluorescently labelled oligonucleotide. In embodiments, the genetically modifying agent is a pathogen. In embodiments, the genetically modifying agent is a virus. In embodiments, the genetically modifying agent is a DNA virus (e.g., pox virus, herpesvirus, adenovirus, parvovirus, or warts virus). In embodiments, the genetically modifying agent is an RNA virus (e.g., influenza virus, rotavirus, mumps virus, rabies virus, eastern equine encephalitis virus, corona virus, LCM virus, polio virus, or HIV virus). In embodiments, the genetically modifying agent is a toxin. In embodiments, the genetically modifying agent is a peptide. In embodiments, the genetically modifying agent is a prion. In embodiments, the genetically modifying agent is a small molecule (e.g., a pharmaceutical agent). [0311] In an aspect is provided a method of identifying a cell that includes a synthetic target. In embodiments, the method includes detecting whether a synthetic target is present in the cell by detecting a plurality of different targets within an optically resolved volume of a cell in situ, according to the methods described herein, including embodiments, and identifying a cell that includes a synthetic target when the presence of the synthetic target is detected in the cell. In embodiments, the method includes contacting a cell or tissue with a probe oligonucleotide and binding an RNA binding sequence of the probe oligonucleotide to an RNA molecule, wherein the probe oligonucleotide further includes a splint binding sequence; extending the RNA binding sequence along the RNA molecule to form a complementary sequence including a first target sequence and a second target sequence; contacting the cell or tissue with a splint oligonucleotide and binding a first sequence of the splint oligonucleotide to the splint binding sequence and binding a second sequence of the splint oligonucleotide to the second target sequence; forming a circular polynucleotide including the first sequence, or a complement thereof, and the second sequence, or a complement thereof; amplifying the circular polynucleotide to generate an amplification product including multiple copies of the first sequence, or a complement thereof, and the second sequence, or a complement thereof; and detecting (e.g., sequencing) the amplification product. In embodiments, the method includes serially cycling through detection cycles to determine the sequence, wherein each detection cycle includes hybridizing, detecting, and removing a fluorescently labelled oligonucleotide. In embodiments the synthetic target is a chimeric antigen receptor (CAR) or a gene that encodes a chimeric antigen receptor (CAR). In embodiments the synthetic target is a target introduced to the cell by genetic engineering methods (e.g., transcription activator-like effector nucleases (TALENs) or clustered regularly interspaced short palindromic repeats (CRISPR) methods).

EXAMPLES

Example 1. T-cell and B-cell receptor repertoire sequencing

[0312] The functions of immune cells such as B- and T-cells are predicated on the recognition through specialized receptors of specific targets (antigens) in pathogens. There are approximately 10¹⁰— 10¹¹ B-cells and 10¹¹ T-cells in a human adult (Ganusov VV, De Boer RJ. Trends Immunol. 2007;28(12):514-8; and Bains I, Antia R, Callard R, Yates AJ. Blood. 2009;113(22):5480-5487) Immune cells are critical components of adaptive immunity in humans. Immune cells (e.g., T cells, B cells, NK cells, neutrophils, and monocytes) directly bind to pathogens through antigenbinding regions present on the cells. Within lymphoid organs (e.g., bone marrow for B cells and the thymus for T cells) the gene segments variable (V), joining (J), and diversity (D) rearrange to produce a novel amino acid sequence in the antigen-binding regions of antibodies that allow for the recognition of antigens from a range of pathogens (e.g., bacteria, viruses, parasites, and worms) as well as antigens arising from cancer cells. The large number of possible V-D-J segments, combined with additional (junctional) diversity, lead to a theoretical diversity of >10¹⁴, which is further increased during adaptive immune responses. Overall, the result is that each B- and T-cell expresses a practically unique receptor, whose sequence is the outcome of both germline and somatic diversity. These antibodies also contain a constant (C) region, which confers the isotype to the antibody. In most mammals, there are five antibody isotypes: IgA, IgD, IgE, IgG, and IgM. For example, each antibody in the IgA isotype shares the same constant region.

[0313] While parts of the B-cell immunoglobulin receptor (BCR) can be traced back to segments encoded in the germline (i.e., the V, D and J segments), the set of segments used by each receptor is something that needs to be determined as it is coded in a highly repetitive region of the genome (Yaari G, Kleinstein SH. Practical guidelines for B-cell receptor repertoire sequencing analysis. Genome Med. 2015;7: 121. (2015)). Additionally, there are no pre-existing full-length templates to align the sequencing reads. Thus, obtaining long-range sequence data is incredibly insightful to gain insights into the adaptive immune response in healthy individuals and in those with a wide range of diseases. Utilizing the methods described herein, comprehensive in situ snapshots of the repertoire diversity for each class of antibody may be realized by using targeted oligonucleotide primers to sequence the C-V-D-J segments in intact B cells.

[0314] In situ sequencing involves tissue and/or cellular extraction, combined with the fixation and permeabilization of cells, followed by amplification of the target nucleic acid fragments for sequencing. Briefly, cells and their surrounding milieu are attached to a substrate surface, fixed, and permeabilized. Targeted oligonucleotide primers designed for C-V-D-J sequencing are then annealed to the nucleic acid of interest or a portion thereof. According to the methods and compositions described herein, the nucleic acid (e.g., mRNAs) present in the cell (depicted as a wavy line, wherein Ml, M2, and M3 represent different mRNA species) are subjected to an amplification technique where a targeted oligonucleotide primer (i.e., target oligonucleotide probe) anneals to the nucleic acid, for example, the mRNA species labeled M2. The target oligonucleotide hybridizes to the mRNA molecule at a region downstream (i.e., an adjacent region in the 3’ direction) of the sequence of interest (i.e., the subject sequence) (FIG. 1A). As shown in FIG. IB, the hybridized target oligonucleotide probe is then extended with a reverse transcriptase (e.g., a strand-displacing reverse transcriptase, shown as a cloud-like object) to generate a cDNA copy of the target nucleic acid including a complement of the subject sequence. The cellular RNA may then be digested (e.g., digested with a ribonuclease, such as RNAse H), and a splint oligonucleotide including regions of complementarity to the oligonucleotide probe and cDNA is hybridized to the extended oligonucleotide probe, as shown in FIG. 1C. As shown in FIG. ID, the 3’ overhang of the extended oligonucleotide probe (i.e., a 3’ tail sequence of the extended oligonucleotide probe including cDNA that is not complementary to the splint oligonucleotide) is then digested (e.g., digested with a single-stranded 3’-5’ exonuclease), and the extended oligonucleotide probe is ligated (not shown) to form a circular polynucleotide. The resulting circular polynucleotide may be primed, e.g., with the 3’ end of the splint oligonucleotide and extended with a strand-displacing polymerase to generate a concatemer containing multiple copies of the target sequence, as depicted in FIG. IE. Alternatively, following hybridization of the splint oligonucleotide to the extended oligonucleotide probe, the 3’ end of the splint oligonucleotide is extended with a polymerase (e.g., a non strand-displacing polymerase) and ligated to form a circular polynucleotide, as shown in FIG. IF. As shown in FIG. 1G, the 3’ overhang of the extended oligonucleotide probe (i.e., a 3’ tail sequence of the extended oligonucleotide probe including cDNA that is not complementary to the splint oligonucleotide) is then digested (e.g., digested with a single-stranded 3’ exonuclease), generating a 3’ end in the extended oligonucleotide probe. The circular polynucleotide may then be primed, e.g., with the 3’ end of the extended oligonucleotide probe and extended with a strand-displacing polymerase to generate a concatemer containing multiple copies of the subject sequence, as depicted in FIG. 1H. This amplification product is then primed with a sequencing primer and subjected to sequencing processes as described herein.

[0315] Optionally, one or more nucleotides within the splint oligonucleotide sequence, the sequencing primer sequence, and/or the target oligonucleotide probe contains one or more functional moieties (e.g., bioconjugate reactive groups) that serve as attachment points to the cell or the matrix in which the cell is embedded (e.g., a hydrogel). In embodiments, one or more nucleotides within the splint oligonucleotide sequence, the sequencing primer sequence, and/or the target oligonucleotide probe contains one or more functional moieties (e.g., bioconjugate reactive groups) that serve as attachment points to complementary bioconjugate reactive groups within the cell (e.g., a protein). In embodiments, a plurality of target oligonucleotide probes and/or splint oligonucleotides are provided to the matrix in which the cell is embedded prior to amplification. In embodiments, a plurality of target oligonucleotide probes and/or splint oligonucleotides are provided to the matrix in which the cell is embedded concurrently with amplification. In embodiments, the bioconjugate reactive group is located at or near the 5’ or 3’ end of the probe, primer, and/or oligonucleotide. In embodiments, the bioconjugate reactive group is located at an internal position of the probe, primer, and/or oligonucleotide e.g., the primer contains one or more modified nucleotides, such as aminoallyl deoxyuridine 5 '-triphosphate (dUTP) nucleotide(s). In embodiments, one or more target oligonucleotide probes may be used to aid in tethering the extension product to a confined area and may not be extended. In embodiments, one or more target oligonucleotide probes may be used to aid in tethering the extension product to a confined area and may also be capable of being extended. For example, one or more immobilized oligonucleotides may be used to aid in tethering the extension product to a localized area and may be extended in an exponential RCA amplification reaction.

[0316] In embodiments, the methods described herein may be utilized for B cell heavy and light chain in situ sequencing by targeting the combination of variable and constant gene segments that make up a given heavy and light chain. These methods provide unique insight into the spatial localization and recombination efforts of a cell’s heavy and light chain genes. Likewise, the methods can be applied for T-cell receptor (TCR) alpha and beta chain in situ sequencing. The genes encoding alpha (TCRA) and beta (TCRB) chains are composed of multiple non-contiguous gene segments which include V, D, and J segments for TCRB and V and J for TCRA. As with B cell receptor diversity, the enormous diversity of TCR repertoires is generated by random combinatorial gene events. The methods described here can be used to provide a comprehensive in situ view of TCR diversity in intact T cells.

Example 2. In situ sequencing with a targeted oligonucleotide primer

[0317] Single-molecule RNA FISH (smFISH) is a versatile assay that allows detecting single RNA molecules with high specificity. In smFISH, a set of typically 30-50 oligonucleotides of 20 nucleotides (nt), each conjugated to a single fluorophore, are hybridized to a complementary RNA target. Individual transcripts are then visualized as diffraction-limited spots using wide-field epifluorescence microscopy, and quantified. A major limitation of this approach, however, is that smFISH signals are dim, while background fluorescence is high in FFPE samples (with large variability depending on the tissue type, sample age, and fixation conditions). Hence, imaging at high magnification (60-100*) is required. As a result, only a very small area of the sample is usually imaged (typically, 40-50 fields of view), making it difficult to assess intratumor heterogeneity. In contrast to smFISH, other methods such as RNAscope, and single-molecule hybridization chain reaction (smHCR) involve one or more steps of signal amplification, which results in brighter fluorescence signals and higher signal-to-noise ratio. However, these methods have a number of drawbacks that limit their utility for the purpose of quantifying the intratumor heterogeneity of clinically relevant biomarkers. The sensitivity of RNAscope is lower compared to smFISH. Fluorescent in situ RNA Sequencing (FISSEQ) is another approach in which RCA products (RCPs) are generated from self-circularized cDNA in a non-targeted fashion, and then sequenced in situ by sequencing-by-ligation (SBL). First, cDNA synthesis is performed using a mix of regular and modified amine-bases, together with tagged random-hexamer RT primers. Via the amine bases, cDNA is cross-linked to its cellular environment and thereafter circularized by ligation. Subsequent RCA creates single stranded DNA nanoballs, whose positions are maintained via cross-linking to the cellular protein matrix. Sequencing is then performed using SBL with a read-length of 30 bases. However, to discriminate many different targets, a partition sequencing strategy is applied by using extended sequencing primers, where nanoballs are randomly sampled so that only a subset is sequenced (see, Asp M et al. Bioessays. 2020; 42(10):el900221, which is incorporated herein by reference in its entirety).

[0318] Recently, a new assay termed RollFISH was developed that integrates the specificity of smFISH with rolling circle amplification (see, e.g., Wu C et al. Commun. Biol. 2018; 1 :209, which is incorporated herein by reference in its entirety). In RollFISH, the design of smFISH probes is modified so that padlock probes can be docked to them, thus enabling signal amplification. Briefly, each RollFISH probe consists of a set of oligonucleotides, each containing a 3 Ont sequence complementary to the RNA target, followed by a 46nt docking sequence orthogonal to the human transcriptome on the 3' end. The oligonucleotide probes are hybridized in situ to their complementary target, followed by removal of unspecifically bound ODNs. Next, a padlock probe containing a transcript-specific barcode sequence is docked to each oligonucleotide probe and circularized in situ to form a single-stranded DNA circle. As in standard RCA, rolling circle amplification is then carried out using the Phi29 polymerase primed by the 3' end of the oligonucleotide probe. The resulting RCA product (RCP) contains hundreds to thousands of copies of the reverse sequence of the transcript-specific barcode sequence, which is detected using a fluorescently labeled secondary probe. Because a RollFISH probe consists of many oligonucleotide probes, multiple RCPs can form simultaneously on the same transcript molecule, resulting in a bright fluorescent spot that can be visualized at low magnification (20x) using widefield epifluorescence microscopy.

[0319] A drawback of the RollFISH design is that the individual padlock probes include the barcode sequence, and thus a unique padlock probe must be designed for each region of nucleic acid of interest being targeted by the oligonucleotide probes. Padlock probes are typically longer oligonucleotides, and thus generating a panel of unique probe for transcriptome detection is an expensive process. An alternate method for detection of target RNA in a sample was recently described that uses a hairpin probe which unfolds upon binding to its target RNA sequence, revealing a 3’ end region which is capable of binding to a circularizable oligonucleotide (see, U.S. Pat. Pub. US 2022/0010348, which is incorporated herein by reference in its entirety). The 3’ end region (i.e., the region that binds to a circularizable oligonucleotide) may include a gap fill sequence for incorporation into the circularizable oligonucleotide. The hairpin probe is also described as including a reporter domain used to distinguish between different target sequences in a target RNA, wherein the reporter domain is in the region of complementarity between the hairpin probe and the circularizable oligonucleotide, such that a different circularizable oligonucleotide is required to detect each reporter domain in the hairpin probe.

[0320] When targeting known regions on a target RNA or DNA molecule, it is possible to design targeted oligonucleotide probes that include a single hybridization sequence complementary to the known nucleic acid sequence, resulting in a shorter oligonucleotide, in comparison with a gap fill PLP that includes two hybridization sequences. Utilizing the methods described herein, efficient and comprehensive in situ sequencing of diverse target populations using a targeted oligonucleotide primer may be realized. Our solution is to use independently targeted oligonucleotides that include a target hybridization sequence (e.g., a target hybridization sequence from a known set of target hybridization sequences) corresponding to the targeted nucleic acid sequence. The target hybridization sequence is designed such that it anneals to a target nucleic acid (e.g., an mRNA molecule) at a region downstream (e.g., in the 3’ direction) from one or more target sequences of interest, enabling the target sequence(s) of interest (i.e., the subject sequence) to be incorporated into the target oligonucleotide probe through a reverse transcription reaction, for example. The extended oligonucleotide probe may then be circularized by splint ligation using a splint oligonucleotide that includes a portion of the target nucleic acid sequence downstream of the target hybridization sequence complement (i.e., a known sequence that is incorporated into the target oligonucleotide primer during reverse transcription). Following circularization, the circular polynucleotide including the subject sequence complement is amplified, and thereafter detected (e.g., detected by sequencing or by hybridization with a labeled probe).

[0321] Compared to FISSEQ, a significant advantage of the approach described herein is that it results in circles of a defined size for all the desired targets. In FISSEQ, the point of ligation is not defined (i.e., the sequence ends that are ligated together to generate a circular oligonucleotide following, for example, reverse transcription). This results in generating a range of circular oligonucleotides of various nucleotide lengths (e.g., 50 to 500 bp), which results in differing rates of amplification. Amplifying circular oligonucleotides with a range of sizes provides heterogeneous signals, resulting in significant fluorescent intensity differences, thereby complicating downstream detection. In addition, larger circular oligonucleotides (e.g., greater than 300, 400, or 500 nucleotides), which will be amplified less during rolling circle amplification compared to smaller circular oligonucleotides, may not produce sufficient amplification product to be detectable. Additionally, the methods described herein do not require performing nuclease digestion after reverse transcription to shorten the cDNA for the purpose of generating smaller circular oligonucleotides.

[0322] With the approaches described herein, targeting a broad panel of transcripts would only require modifying the nucleotide sequence of the targeted oligonucleotide probes and target sequence of the splint oligonucleotide. Since such an oligonucleotide is typically shorter than, for example, a gap fill PLP, reduced costs would be realized. An additional advantage of this approach is that circularization of a gap fill PLP is typically more efficient when using a DNA template rather than an RNA template. By using targeted oligonucleotide probes and splint oligonucleotides that consist primarily of DNA, high efficiency ligation and circularization of the extended oligonucleotide probe is achieved, leading to increased amplification product formation. The present methods include the advantage of not having to perform reverse transcription of a target RNA molecule to generate cDNA, for example, as the polynucleotide probe can directly hybridize to RNA, and as described herein, the splint oligonucleotide can subsequently hybridize to the polynucleotide probe (e.g., a polynucleotide probe consisting of DNA).

Method A: Amplification from the splint oligonucleotide

[0323] In situ sequencing involves tissue and/or cellular extraction, combined with the fixation and permeabilization of cells, followed by amplification of the target nucleic acid fragments for sequencing. Briefly, cells and their surrounding milieu are attached to a substrate surface, fixed, and permeabilized. Targeted oligonucleotide probes designed for RNA detection are then annealed to an endogenous nucleic acid (e.g., a mRNA molecule). For example, mRNA is targeted with a set of oligonucleotides targeting one or more regions of interest (e.g., up to 24, or up to 48 regions per gene). FIG. 3 A illustrates hybridizing a target oligonucleotide probe to a target nucleic acid sequence (e.g., a probe hybridization sequence of an mRNA molecule), wherein the target hybridization sequence is located at a 3’ end of the target oligonucleotide probe. The probe hybridization sequence is located downstream (i.e., in the 3’ direction) of a subject sequence (e.g., a subject sequence of the mRNA molecule that includes the sequence information of interest for downstream assays, such as in in situ sequencing). Upstream (i.e., in the 5’ direction) of the subject sequence is the target sequence. Following hybridization of the oligonucleotide probe, the 3’ end is extended with, e.g., a strand-displacing reverse transcriptase such as M-MLV or SSIV RT, to generate an extended oligonucleotide probe including a copy of the subject sequence (i.e., a subject sequence complement) and target sequence (i.e., a target sequence complement). In some embodiments, additional sequence(s) upstream of the target sequence (referred to herein as a “tail sequence”) are also incorporated into the extended oligonucleotide probe. RNA digestion, e.g., with a ribonuclease such as RNAse H, may be performed to remove the target mRNA, leaving behind the extended oligonucleotide probe with a 3’ end, as shown in FIG. 3B.

[0324] In embodiments, a splint oligonucleotide as illustrated in FIGS. 2B or 2C is then hybridized to the extended oligonucleotide probe as illustrated in FIG. 3C, wherein the probe sequence complement at the 5’ end of the splint oligonucleotide is hybridized to the probe sequence at the 5’ end of the extended oligonucleotide probe, and the target sequence at the 3’ end of the splint oligo is hybridized to the target sequence complement of the extended oligonucleotide primer. In embodiments, a 3’ overhang of the extended oligonucleotide probe (e.g., the tail sequence complement) is generated following hybridization of the splint oligonucleotide due to the presence of non-complementary sequence. Exonuclease digestion of the tail sequence complement using a single-stranded 3’-5’ exonuclease (e.g., Exonuclease I; shown as a circular partition) is then performed, as shown in FIG. 3D, digesting the 3’ overhang region of the extended oligonucleotide probe. The 5’ end and 3’ end of the extended oligonucleotide probe are then ligated (e.g., ligated with T4 DNA ligase) to generate a circular polynucleotide. Using the splint oligonucleotide as an amplification primer, rolling circle amplification may be performed with a strand-displacing polymerase (e.g., a phi29 polymerase, shown as a cloud-like object) to generate a concatemer including multiple copies of the subject sequence, for example, as shown in FIG. 3E. Additional amplification primers may be hybridized to the amplification product (e.g., to one or more primer binding sequences, or complements thereof) of FIG. 3E and extended, thereby generating additional amplification products. A sequencing primer, for example, is then hybridized to the amplification product(s) and detection by sequencing is performed. We proceeded to use the methods described herein to perform in situ spatial sequencing using a target oligonucleotide primer specific for a cellular mRNA.

[0325] Plating and Fixation: All steps were performed in 96-well plate format. Cell suspensions were centrifuged for 5 min at 0.3 ref and resuspended in IX PBS prior to plating. Cells were plated at a density of 50,000 live cells/well and allowed to settle at the bottom of the plate for at least 30 min at 4° C. Cells were then fixed with 4% formaldehyde in IX PBS for 20 min at room temperature (RT), and washed 3 times with IX PBS to remove the formaldehyde. Cells were then permeabilized with 0.5% Triton X-100 in lx PBS for 20 min at RT, then washed lx with lx PBS and 2x with TEL hybridization buffer (20% formamide and lx TELsoo in water). [0326] Target Probe Hybridization: Primers specific for the FR4 region flanking the CDR3 sequence of a target VDJ transcript were added at a final concentration of 1 pM in TEL hybridization buffer and incubated for 30 min at 60° C followed by incubation for 90 min at 37° C.

[0327] Reverse Transcription: To incorporate the target mRNA sequence into the DNA oligonucleotide primer, SuperScript IV™ reverse transcriptase (Thermo Fisher Catolog # 18090010) was added at a final concentration of 4 U/pL with dNTPs (0.5 mM each), 0.125 mM aminoallyl-dUTP, 75mM LiCl, 3mM MgCh, and 0.2 U/pL SUPERase-In™ RNase inhibitor (Thermo Fisher Catalog # AM2694) in lx V5 buffer, pH 8.0 and incubated for 2 hrs at 37° C. Cells were then washed 3x with lx PBS.

[0328] RNA Digestion: RNAse H was then added at a final concentration of 0.4 U/pL in lx PBS and incubated for 1 hr at RT. Cells were then washed lx with lx PBS, and 1 M Tris (pH 8.0) added and incubated for 15 min at RT. Cells were then washed lx with lx PBS and 2x with SSC hybridization buffer (2x SSC and 20% formamide in water).

[0329] Splint Hybridization: Splint oligonucleotide was added at a final concentration of 1 pM in SSC hybridization buffer. The splint oligonucleotide included a sequence complementary to the FR3 region adjacent to the CDR3 sequence of the target mRNA. The splint oligonucleotide was then allowed to hybridize for 2 hrs at 37° C. The cells were then washed lx with SSC hybridization buffer for 5 min at 37° C and 2x with lx PBS for 5 min each at 37° C.

[0330] Exonuclease digestion: Exonuclease I (New England BioLabs Catalog #M0293S) was added at a final concentration of 0.1 U/pL in lx Exonuclease I Reaction Buffer (New England BioLabs) and incubated for 1 hr at 37° C. The cells were then washed lx with SSC hybridization buffer for 5 min at 37° C and 2x with lx PBS for 5 min each at 37° C.

[0331] Ligation: Following the washes, T4 DNA ligase (New England Biolabs Catalog # M0202S) was added at a final concentration of 24 U/pL and incubated for 2 hrs at 37° C to circularize the extended target oligonucleotide primer. Cells were then washed lx with lx PBS and 2x with SSC hybridization buffer.

[0332] Rolling Circle Amplification: Splint oligonucleotide was added at a final concentration of 1 pM in SSC hybridization buffer and incubated for 1 hr at 37° C. Cells were then washed lx with hybridization buffer and 2x with lx PBS. A mutant version of phi29 DNA polymerase was then added at a final concentration of 0.45 pM with 1 M betaine, dNTPs (0.5 mM each), 0.125 mM aminoallyl-dUTP, 0.2 mg/mL BSA, 4 mM DTT, and 0.2 U/pL SUPERase-In™ RNase inhibitor in DEPC-treated water and incubated overnight (i.e., at least 16 hours) at 37° C. Cells were then washed 3x with lx PBS.

[0333] Detection: TetraSpeck™ microspheres were added to crosslinked cells at a final concentration of 0.1 nM in PBST (0.1% Tween-20 in lx PBS) and allowed to settle for at least 30 min at RT, or centrifuged for 3 min at 2,000 RPM. Sequencing primer targeting the CDR3 region of the amplification product was then added at a final concentration of 0.5 pM in hybridization buffer and incubated for 30 min at 37° C. The cells were then washed 3x with flow cell wash buffer, and sequencing-by-synthesis performed.

[0334] Following the workflow outlined above, we performed in situ sequencing of an IgH transcript in Ramos Burkitt’s lymphoma cells, as shown in FIG. 4. Three sequencing cycles were performed in one well of a 96-well plate, wherein the target oligonucleotide probe was targeted to the FR4 region adjacent to a CDR3 sequence in an IgH transcript. Each tile of FIG. 4 represents each of the first three sequencing cycles using a sequencing primer targeting a 3’ end of the CDR3 region of the RCA product. The highlighted tiles shown in FIG. 4 indicate the base detected during each sequencing cycle in the outlined cell, wherein the sequence ‘TCC’ was detected. This example demonstrates the ability to perform at least 3 in situ sequencing cycles in a single-cell using the methods described herein for reverse transcription with a targeted primer, and circularization and amplification with a splint oligonucleotide. We estimate that each well of a 96- well plate (as shown in FIG. 4) can hold approximately 55,000 cells, so these methods could be applied to sequencing about 5.3 million cells in a single 96-well plate, which can be automated for high-throughput processing.

Method B: Amplification from the splint oligonucleotide

[0335] As an alternative to Method A described supra, we also performed in situ sequencing following amplification as illustrates in FIGS. 3A-3C and 3F-3G. Briefly, cells and their surrounding milieu are attached to a substrate surface, fixed, and permeabilized. Targeted oligonucleotide probes designed for RNA detection are then annealed to nucleic acid regions of interest. For example, mRNA is targeted with a set of oligonucleotide probes targeting one or more regions of interest (e.g., up to 24, or up to 48 regions per gene). FIG. 3 A illustrates hybridizing a target oligonucleotide probe to a target nucleic acid sequence (e.g., a probe hybridization sequence of an mRNA molecule), wherein the target hybridization sequence is located at a 3’ end of the target oligonucleotide probe. The probe hybridization sequence is located downstream (i.e., in the 3’ direction) of a subject sequence (e.g., a subject sequence of the mRNA molecule that includes the sequence information of interest for downstream assays, such as in in situ sequencing). Upstream (i.e., in the 5’ direction) of the subject sequence is the target sequence. Following hybridization of the oligonucleotide probe, the 3’ end is extended with, e.g., a strand-displacing reverse transcriptase such as M-MLV or SSIV RT, to generate an extended oligonucleotide probe including a copy of the subject sequence (i.e., a subject sequence complement) and target sequence (i.e., a target sequence complement). In some embodiments, additional sequence(s) upstream of the target sequence (referred to herein as a “tail sequence”) are also incorporated into the extended oligonucleotide probe. RNA digestion, e.g., with a ribonuclease such as RNAse H, may be performed to remove the target mRNA, leaving behind the extended oligonucleotide probe with a 3’ end, as shown in FIG. 3B.

[0336] A splint oligonucleotide as illustrated in FIG. 2C is then hybridized to the extended oligonucleotide probe as illustrated in FIG. 3C, wherein the probe sequence complement at the 5’ end of the splint oligonucleotide is hybridized to the probe sequence at the 5’ end of the extended oligonucleotide probe, and the target sequence at the 3’ end of the splint oligo is hybridized to the target sequence complement of the extended oligonucleotide primer, after hybridizing the splint oligonucleotide (e.g., the splint oligo illustrated in FIG. 2C) to the extended oligonucleotide probe, the 3’ end of the splint oligonucleotide is extended using a non-strand displacing polymerase (e.g., T4 DNA polymerase, illustrated as a cloud-like object), generating an extended splint oligonucleotide including the subject sequence, probe hybridization sequence, and probe sequence complement. The 5’ and 3’ ends of the extended splint oligonucleotide are then ligated (e.g., ligated with T4 DNA ligase) to form a circularized polynucleotide. Exonuclease digestion of the tail sequence complement using a single-stranded 3’-5’ exonuclease (e.g., Exonuclease I; shown as a circular partition) is then performed, as shown in FIG. 3G, digesting the 3’ overhang region of the extended oligonucleotide probe and generating a 3’ end (i.e., a 3’ end duplex with the circular polynucleotide). The duplexed 3’ end of the extended oligonucleotide probe may then be used as an amplification primer for rolling circle amplification with a strand displacing polymerase (e.g., a phi29 polymerase, illustrated as a cloud-like object), generating a concatemer including multiple copies of the subject sequence complement, for example. Additional amplification primers may be hybridized to the amplification product (e.g., to one or more primer binding sequences, or complements thereof) of FIG. 3G and extended, thereby generating additional amplification products. A sequencing primer, for example, is then hybridized to the amplification product and detection by sequencing is performed. We proceeded to use the methods described herein to perform in situ spatial sequencing using a target oligonucleotide primer specific for a cellular mRNA. [0337] Plating and Fixation: All steps were performed in 96-well plate format. Cell suspensions were centrifuged for 5 min at 0.3 ref and resuspended in IX PBS prior to plating. Cells were plated at a density of 50,000 live cells/well and allowed to settle at the bottom of the plate for at least 30 min at 4° C. Cells were then fixed with 4% formaldehyde in IX PBS for 20 min at room temperature (RT), and washed 3 times with IX PBS to remove the formaldehyde. Cells were then permeabilized with 0.5% Triton X-100 in lx PBS for 20 min at RT, then washed lx with lx PBS and 2x with TEL hybridization buffer (20% formamide and lx TELsoo in water).

[0338] Target Probe Hybridization: Primers specific for the FR4 region flanking the CDR3 sequence of a target VDJ transcript were added at a final concentration of 1 pM in hybridization buffer and incubated for 30 min at 60° C followed by incubation for 90 min at 37° C.

[0339] Reverse Transcription: To incorporate the target mRNA sequence into the DNA oligonucleotide probe, SuperScript IV™ reverse transcriptase (Thermo Fisher Catolog # 18090010) was added at a final concentration of 4 U/pL with dNTPs (0.5 mM each), 0.125 mM aminoallyl-dUTP, 75mM LiCl, 3mM MgCh, and 0.2 U/pL SUPERase-In™ RNase inhibitor (Thermo Fisher Catalog # AM2694) in lx V5 buffer, pH 8.0 and incubated for 2 hrs at 37° C. Cells were then washed 3x with lx PBS.

[0340] RNA Digestion: RNAse H was then added at a final concentration of 0.4 U/pL in lx PBS and incubated for 1 hr at RT. Cells were then washed lx with lx PBS, and 1 M Tris (pH 8.0) added and incubated for 15 min at RT. Cells were then washed lx with lx PBS and 2x with SSC hybridization buffer (2x SSC and 20% formamide in water).

[0341] Splint Hybridization: Splint oligonucleotide was added at a final concentration of 1 pM in SSC hybridization buffer. The splint oligonucleotide included a sequence complementary to the FR3 region adjacent to the CDR3 sequence of the target mRNA, and a 10 nucleotide (e.g., 10 adenine) spacer sequence. The splint oligonucleotide was then allowed to hybridize for 2 hrs at 37° C. The cells were then washed lx with SSC hybridization buffer for 5 min at 37° C and 2x with lx PBS for 5 min each at 37° C.

[0342] Exonuclease digestion: Exonuclease I (New England BioLabs Catalog #M0293S) was added at a final concentration of 0.1 U/pL in lx Exonuclease I Reaction Buffer (New England BioLabs) and incubated for 1 hr at 37° C. The cells were then washed lx with SSC hybridization buffer for 5 min at 37° C and 2x with lx PBS for 5 min each at 37° C.

[0343] Ligation: Following the washes, T4 DNA ligase (New England Biolabs Catalog # M0202S) was added at a final concentration of 24 U/pL and incubated for 2 hrs at 37° C to circularize the extended target oligonucleotide primer. Cells were then washed lx with lx PBS and 2x with SSC hybridization buffer.

[0344] Rolling Circle Amplification: Splint oligonucleotide was added at a final concentration of 1 pM in SSC hybridization buffer and incubated for 1 hr at 37° C. Cells were then washed lx with hybridization buffer and 2x with lx PBS. A mutant version of phi29 DNA polymerase was then added at a final concentration of 0.45 pM with 1 M betaine, dNTPs (0.5 mM each), 0.125 mM aminoallyl-dUTP, 0.2 mg/mL BSA, 4 mM DTT, and 0.2 U/pL SUPERase-In™ RNase inhibitor in DEPC-treated water and incubated overnight (i.e., at least 16 hours) at 37° C. Cells were then washed 3x with lx PBS.

[0345] Detection: TetraSpeck™ microspheres were added to crosslinked cells at a final concentration of 0.1 nM in PBST (0.1% Tween-20 in lx PBS) and allowed to settle for at least 30 min at RT, or centrifuged for 3 min at 2,000 RPM. Sequencing primer targeting the CDR3 region of the amplification product was then added at a final concentration of 0.5 pM in hybridization buffer and incubated for 30 min at 37° C. The cells were then washed 3x with flow cell wash buffer, and sequencing-by-synthesis performed.

[0346] Following the workflow outlined above, we performed in situ sequencing of an IgH transcript in Ramos Burkitt’s lymphoma cells, as shown in FIG. 5. Three sequencing cycles were performed in one well of a 96-well plate, wherein the target oligonucleotide probe was targeted to the FR4 region adjacent to a CDR3 sequence in an IgH transcript. Each tile of FIG. 5 represents each of the first three sequencing cycles using a sequencing primer targeting a 3’ end of the CDR3 region of the RCA product. The highlighted tiles shown in FIG. 5 indicate the base detected during each sequencing cycle in the outlined cell, wherein the sequence ‘ AGT’ was detected. This example demonstrates the ability to perform at least 3 in situ sequencing cycles in a single-cell using the methods described herein for reverse transcription with a targeted primer, and circularization and amplification with a splint oligonucleotide including a spacer sequence.

[0347] Imaging: Either 2D or 3D fluorescent imaging modalities can be used. An advantage of 3D imaging is that a larger number of individual volumes can be resolved. 3D fluorescent imaging methods include confocal microscopy, light sheet microscopy, and multi-photon microscopy. For example, if the imaging system has a lateral resolution of 0.5 um, and a depth resolution of 1.0 um, a 10x10x10 um volume would contain 20x20x10 = 4,000 voxels. If each voxel can resolve 10 barcodes, then this would correspond to a capacity of 40,000 reads in a 10- um cube without pushing the limits of optical resolution. [0348] Further information can be gained by including expansion microscopy if subcellular resolution is required beyond the limits of diffraction, or if an even larger number of reads is desired.

[0349] The described methods can be applied to single cells affixed to a transparent substrate, as well as to sections of tissue on a similar substrate. In both cases (individual cells or cells in tissue), the cells may be fixed and permeabilized for delivering probes, enzymes, nucleotides and other components required in the reactions.

EXAMPLE 3: Detection of oncogenic gene variants

[0350] The concept of precision oncology aims to address the need for molecular characterization of individual tumors to enable tailored treatment for each patient. Intratumoral heterogeneity, evident from the varied therapeutic sensitivity existing in multiple subclones from within the same tumor, has made the application of precision oncology more difficult. Breast cancer has been reported to display both inter- and intra-tumoral genetic heterogeneity with thousands of different mutations uniquely combined in each tumor and subclone. Breast cancer diagnostics typically relies on a combined evaluation of histopathology including tumor grade and immunohistochemical staining of ER, PR, HER2, and Ki67. Additionally, complementary molecular analyses such as NGS, Mammaprint, OncotypeDX, and PAM50 are done on bulk cell lysates from homogenized tissues. Bulk tissue-based analytical approaches do not provide high levels of resolution into the effects of genetic heterogeneity on complex tumor cell interactions such as epithelial-to-mesenchymal transition, angiogenesis, and invasiveness. Spatially resolving techniques like in situ sequencing as described herein allow for in-depth characterization of the different cellular niches and their signaling pathways within tumor tissue. This spatial information, combined with classical histological diagnostics, can couple molecular features directly to tumor morphology.

[0351] HER2 is a driver gene in breast cancer, and HER2 amplification is the predictive marker and molecular target of anti-HER2 agents such as trastuzumab, pertuzumab, or lapatinib (Montemurro and Scaltriti, 2014). Approximately 20-25% of all breast cancers overexpress HER2 (referred to as HER2-positive) and are linked to an aggressive phenotype. Oncogenic mutations in HER2 have been suggested to contribute to anti-HER2 therapy resistance. Several HER2 mutations in the tyrosine-kinase domain spanning exon 20 have been described as having an impact on the clinical sensitivity to trastuzumab and lapatinib treatment. Having an in situ transcriptomic profile of a HER2-positive breast cancer with the methods described herein would not only provide spatial expression data, but also inform clinicians regarding the prevalence of mutant oncogene subtypes, such as treatment-resistant HER2 cells.

[0352] The methods described herein provide a in situ sequencing approach for obtaining detailed genomic information from tumor tissue, connecting genetic heterogeneity to pathological manifestation of a cancer, for example HER2 exon 20 expression and sequence identity in breast cancer tissues and cells. Briefly, a tumor tissue section is attached to a substrate surface, fixed, and permeabilized according to known methods in the art. Targeted oligonucleotide probes designed for HER2 exon 20 sequencing are then annealed to complementary regions of the nucleic acid molecule of interest or a portion thereof. In embodiments, the oligonucleotide probe hybridizes to regions adjacent (i.e., the region that flank the target nucleic acid sequence, or a portion thereof) to the target nucleic acid sequence, referred to as the first and the second complementary regions. In the presence of a polymerase, the complement of the target sequence is generated by extending from the first complementary region. A circular polynucleotide is then formed, as described elsewhere herein. The resulting circularized oligonucleotide is primed with an amplification primer and extended with a strand-displacing polymerase to generate a concatemer containing multiple copies of the target nucleic acid sequence. This extension product is then primed with a sequencing primer and subjected to sequencing processes as described herein, thereby providing a high-resolution view of molecular features that can be combined with additional histological findings for clinical decision-making.

[0353] As an alternative or companion diagnostic to a tumor tissue biopsy, the methods described herein may also be applied to isolated circulating tumor cells (CTCs). CTCs are the rare metastatic cancer cells shed from the primary tumor into the circulatory system that can ultimately lead to the formation of metastases. Briefly, CTCs are enriched from whole blood using methods known in the art, then are attached to a substrate surface, fixed, and permeabilized. Targeted oligonucleotide probes designed for genes of interest, e.g., a HER2 gene, a BCL2 gene, an ERG gene, a PTEN gene, are then annealed to flanking complementary regions of the nucleic acid of interest or a portion thereof. Extension, ligation, amplification, and sequencing are then performed as described herein and in Examples 1 and 2. These methods would help distinguish CTCs from contaminating blood cells in situ and provide insight into tumor molecular heterogeneity.

EXAMPLE 4: Monitoring transcriptional response to pharmacological agents

[0354] Large projects such as the Cancer Cell Line Encyclopedia and Genomics of Drug

Sensitivity in Cancer (GDSC) have analyzed hundreds of cancer cell lines and generated data on the genotypes and cellular responses to pharmacological treatment. Additional work has combined multi-omics approaches (e.g., RNA-seq and ATAC-seq) from drug-treated lung cancer cell lines to profile cellular responses and identify novel drug targets. Similar approaches using bulk and single-cell transcriptomics in fibroblasts and mononuclear phagocytes, challenged with immune stimuli such as a genetically modifying agent, revealed that transcriptionally diverging genes like cytokines and chemokines varied in expression across cells. Studies such as these have taken an initial step at mapping the cellular response to therapeutic agents but lack resolution into the dynamic cellular and subcellular heterogeneity of the cellular programs governing downstream physiological effects.

[0355] In gastric cancer (GC), genomic profiling is used to define clinical subtypes based on mutational status of oncogenes such as ERBB2, KRAS, TP53, and PIK3CA. Tumor heterogeneity has profound implications for therapy selection. In a clinical trial testing FGFR2 inhibition in GC, durable responses were observed only in high-level FGFR2 clonally amplified tumors, as assessed by FISH-based in situ heterogeneity mapping. A comparison of paired FGFR2 expression at baseline and 15 days post-treatment further showed significant decreases in FGFR2 mRNA only in the sub-clonal, heterogeneously amplified tumor, possibly reflecting clonal selection of non-amplified compartments as a result of therapeutic pressure. The sequencing methods described herein can be applied to the molecular profiling of a GC tumor to monitor whether FGFR2 expression is perturbed during therapy.

[0356] Briefly, tumor cells obtained from a GC patient before, during, and/or after pharmacological treatment are attached to a substrate surface, fixed, and permeabilized according to known methods in the art. Targeted oligonucleotide probes for FGFR are then annealed to the nucleic acid of interest. As described elsewhere, the target sequence is incorporated into a circular polynucleotide. The resulting circularized oligonucleotide is primed with an amplification primer and extended with a strand-displacing polymerase to generate a concatemer containing multiple copies of the target nucleic acid sequence. This extension product is then primed with a sequencing primer and subjected to a detection processes described herein.

[0357] Such methods may be applied to assess whether a patient being treated for any physiological or psychological condition that requires a pharmacological agent has a transcriptional response in a target cell type that may be indicative of the clinical efficacy of the treatment. These can also provide temporal information for patients under short- or long-term drug treatment to provide relevant clinical information, for instance, gene signatures indicative of drug resistance. Additionally, the methods herein may be used to detect genetic rearrangements at the RNA level, such as splice variants, gene fusions, and inter- and intrachromosomal translocations, both at baseline and during/after treatment of a subject with a pharmacological agent (e.g., a genetically modifying agent). The presence of such genetic rearrangements can also be informative with regards to drug resistance. Less-invasive options for such a diagnostic tool include isolation of CTCs or isolation of immune cells from whole blood or bodily fluids.

EXAMPLE 5: Profiling genome editing efficiency

[0358] The evolution of gene editing towards clinical practice has developed through recent advancements in programmable nucleases, such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas-associated nucleases. Targeted DNA alterations begin with the generation of nuclease-induced double-stranded breaks (DSBs), which lead to the stimulation of DNA recombination mechanisms in mammalian cells. Nuclease-induced DNA DSBs can be repaired by one of the two major mechanisms present in eukaryotic cells: non-homologous end joining (NHEJ) and homologous recombination (HR), resulting in gene disruptions or targeted integration, respectively. The CRISPR-Cas systems are divided into two classes based on the structural variation of the Cas genes and their organization style. Specifically, class 1 CRISPR- Cas systems consist of multiprotein effector complexes, where class 2 systems includes only a single effector protein; at least six CRISPR-Cas types and 29 subtypes are known presently. The most frequently used subtype of CRISPR system is the type 2 CRISPR/Cas9 system, which depends on a single Cas protein from Streptococcus pyogenes (SpCas9) targeting DNA sequences. A single-stranded guide RNA (sgRNA) and a Cas9 endonuclease form a targeting complex, wherein the sgRNA binds to the target sequence and Cas9 precisely cleaves the DNA to generate a DSB and subsequently activate cellular repair programs. Conveniently, changing the sgRNA sequence allows the targeting of new sites, without requiring changes to the Cas9 protein.

[0359] Specific delivery methods have been developed for targeting both Cas9 and sgRNAs directly to the organ of interest in vivo, including direct transfection, lentiviral and adeno- associated virus (AAV)-based transduction, and nanoparticle delivery. Cells may also be isolated from a patient to be treated, edited, and then re-engrafted back to the patient. Such an approach is used in the preparation of chimeric antigen receptor (CAR) T cells for cancer immunotherapy, wherein the patient’s T cells are isolated, reengineered and modified with tumor-antigen-specific receptors and co-stimulating molecules, transduced with a CAR viral vector, amplified, and then infused back into the patient. Furthermore, the development of allogeneic universal “off-the- shelf’ CAR-T cells has been demonstrated effectively using a one-shot CRISPR protocol to knockout endogenous TCR and HLA class 1 molecules. [0360] Determining whether the cell of interest has been successfully targeted by a genome editing endonuclease is traditionally performed via bulk harvesting of cell lysate and analysis of total genomic material. Some of the current challenges in therapeutic targeting involve increasing the specificity of gene correction, improving the efficiency of nuclease editing, and optimizing the delivery systems. By using the in situ sequencing methods described herein, high-resolution information is obtained to decipher the effectiveness of a genome editing treatment, for example, the production of allogeneic CAR T cells.

[0361] Briefly, a population of T cells is subjected to a genome editing technique, for example CRISPR/Cas9, to knockout the TCR and HLA class 1 loci. The cells are then attached to a substrate surface, fixed, and permeabilized according to known methods in the art. Targeted oligonucleotide probes for the TCR and HLA class 1 loci are then annealed to the nucleic acid molecule, and the target sequence is incorporated into a circular polynucleotide as described herein. The resulting circularized oligonucleotide is primed with an amplification primer and extended with a strand-displacing polymerase to generate a concatemer containing multiple copies of the target nucleic acid sequence.

EMBODIMENTS

[0362] Embodiment Pl. A method of generating a complex comprising a circular polynucleotide in a cell, said method comprising: i) hybridizing a splint oligonucleotide to an extended oligonucleotide probe, thereby forming a complex, wherein said splint oligonucleotide comprises a probe sequence complement and a target sequence, wherein said probe sequence complement of said splint oligonucleotide hybridizes to a probe sequence of said extended oligonucleotide probe, wherein said target sequence of said splint oligonucleotide hybridizes to a target sequence complement of said extended oligonucleotide probe, and wherein a subject sequence complement is located between said probe sequence and said target sequence complement of said extended oligonucleotide probe; ii) extending the splint oligonucleotide of said complex along the extended oligonucleotide probe with a polymerase to generate an extended splint oligonucleotide comprising a complement of said subject sequence; and iii) circularizing the extended splint oligonucleotide by ligating the extended splint oligonucleotide to the splint binding sequence of said oligonucleotide probe, thereby forming said complex comprising said circular polynucleotide.

[0363] Embodiment P2. The method of Embodiment Pl, wherein prior to step i) the method further comprises hybridizing an oligonucleotide probe to a target polynucleotide in a cell, said target polynucleotide comprising, from 5’ to 3’, said target sequence, said subject sequence, and a probe hybridization sequence, wherein said probe hybridization sequence is complementary to a 3’ end of said oligonucleotide probe, and extending said oligonucleotide probe along said target polynucleotide with a polymerase to generate said extended oligonucleotide probe.

[0364] Embodiment P3. The method of Embodiment Pl or P2, further comprising amplifying the circular polynucleotide, thereby generating an amplification product comprising multiple copies of said subject sequence complement.

[0365] Embodiment P4. The method of Embodiment P3, wherein amplifying the circular polynucleotide comprises hybridizing a primer to said circular polynucleotide and extending said primer with a strand-displacing polymerase.

[0366] Embodiment P5. The method of Embodiment P3, wherein amplifying the circular polynucleotide comprises contacting the complex with an exonuclease enzyme and generating a 3’ end of the extended oligonucleotide probe, wherein said exonuclease enzyme removes a portion of said complementary sequence, and extending said 3’ end with a strand-displacing polymerase.

[0367] Embodiment P6. The method of Embodiment P4 or P5, wherein extending comprises incubating the circular polynucleotide with a strand-displacing polymerase for about 15 minutes to about 2 hours.

[0368] Embodiment P7. The method of Embodiment P4 or P5, wherein extending comprises incubating the circular polynucleotide with a strand-displacing polymerase for about 30 minutes to about 60 minutes.

[0369] Embodiment P8. The method of any one of Embodiments Pl to P7, wherein the probe sequence of said oligonucleotide probe further comprises a primer sequence.

[0370] Embodiment P9. The method of Embodiment P8, wherein amplifying further comprises contacting the amplification product with an amplification primer comprising a primer sequence complement, hybridizing the amplification primer the primer sequence complement, and extending the amplification primer with a strand-displacing polymerase, thereby generating a second amplification product.

[0371] Embodiment P10. The method of Embodiment P9, wherein the splint oligonucleotide, the amplification primer, or both the splint oligonucleotide and the amplification primer are immobilized to a cellular component. [0372] Embodiment Pl 1. The method of any one of Embodiments Pl to PIO, wherein said target polynucleotide comprises RNA.

[0373] Embodiment P12. The method of any one of Embodiments Pl to Pl 1, wherein said polymerase is a reverse transcriptase.

[0374] Embodiment P13. The method of any one of Embodiments Pl to Pl 2, wherein prior to step i), the method further comprises removing said target polynucleotide.

[0375] Embodiment P14. The method of Embodiment Pl 3, wherein removing said target polynucleotide comprises contacting said target polynucleotide with a ribonuclease.

[0376] Embodiment Pl 5. The method of any one of Embodiments Pl to Pl 4, further comprising detecting the amplification product.

[0377] Embodiment Pl 6. The method of Embodiment Pl 5, wherein detecting the amplification product comprises hybridizing an oligonucleotide associated with a detectable label to the amplification product and identifying said detectable label.

[0378] Embodiment Pl 7. The method of any one of Embodiments Pl to P14, further comprising sequencing the amplification product.

[0379] Embodiment Pl 8. The method of Embodiment P17, wherein sequencing comprises sequencing by synthesis, sequencing by binding, sequencing by ligation, or pyrosequencing.

[0380] Embodiment Pl 9. The method of Embodiment Pl 7, wherein sequencing comprises extending a sequencing primer by incorporating a labeled nucleotide or labeled nucleotide analogue, and detecting the label to generate a signal for each incorporated nucleotide or nucleotide analogue, wherein the sequencing primer is hybridized to the extension product.

[0381] Embodiment P20. The method of Embodiment Pl 9, wherein said sequencing primer comprises a sequence of said subject sequence.

[0382] Embodiment 21. The method of any one of Embodiments Pl to P20, wherein said target polynucleotide is in said cell.

[0383] Embodiment P22. The method of any one of Embodiments Pl to P21, wherein said oligonucleotide probe and said splint oligonucleotide are in said cell.

[0384] Embodiment P23. The method of Embodiment P21 or P22, wherein said cell is permeabilized and immobilized to a solid support surface. [0385] Embodiment P24. A method of generating a complex comprising a circular polynucleotide in a cell, said method comprising: a) hybridizing a splint oligonucleotide to an extended oligonucleotide probe, thereby forming a complex, wherein said splint oligonucleotide comprises a probe sequence complement and a target sequence, wherein said probe sequence complement of said splint oligonucleotide hybridizes to a probe sequence of said extended oligonucleotide probe, wherein said target sequence of said splint oligonucleotide hybridizes to a target sequence complement of said extended oligonucleotide probe, and wherein a subject sequence complement is located between said probe sequence and said target sequence complement of said extended oligonucleotide probe; b) contacting the complex with an exonuclease enzyme and generating an extended oligonucleotide probe comprising a 3’ end, wherein said exonuclease enzyme removes a single-stranded portion of the complex; and c) ligating the probe sequence to the 3’ end of the extended oligonucleotide probe, thereby generating a complex comprising a circular oligonucleotide.

[0386] Embodiment 25. The method of Embodiment P24, wherein prior to step a) the method further comprises hybridizing an oligonucleotide probe to a target polynucleotide in a cell, said target polynucleotide comprising, from 5’ to 3’, said target sequence said subject sequence, and a probe hybridization sequence, wherein said probe hybridization sequence is complementary to a 3’ end of said oligonucleotide probe, and extending said oligonucleotide probe along said target polynucleotide with a polymerase to generate said extended oligonucleotide probe.

[0387] Embodiment P26. The method of Embodiment P24 or P25, further comprising amplifying the circular polynucleotide, thereby generating an amplification product comprising multiple copies of said subject sequence.

[0388] Embodiment P27. A complex comprising: i) a circular polynucleotide comprising a probe sequence, a target hybridization sequence, a subject sequence complement, and a target sequence complement; and ii)a splint oligonucleotide hybridized to said circular polynucleotide, wherein said splint oligonucleotide comprises a probe sequence complement hybridized to said probe sequence of said circular polynucleotide, and wherein said splint oligonucleotide comprises a target sequence hybridized to said target sequence complement of said circular polynucleotide.

[0389] Embodiment P28. The complex of Embodiment P27, wherein said circular polynucleotide further comprises a single-stranded sequence at a 3’ end. [0390] Embodiment P29. The complex of Embodiment P27 or P28, wherein said splint oligonucleotide further comprises a spacer sequence between said target sequence and said probe sequence complement.

[0391] Embodiment P30. The complex of any one of Embodiments P27 to P29, wherein said probe sequence of said circular polynucleotide comprises one or more primer binding sequences.

[0392] Embodiment P31. The complex of any one of Embodiments P27 to P30, wherein said subject sequence complement of said circular polynucleotide comprises a sequencing primer binding sequence.

[0393] Embodiment P32. A kit comprising: a) an oligonucleotide probe comprising a target hybridization sequence and a probe sequence, wherein said target hybridization sequence is complementary to a probe hybridization sequence in a target polynucleotide; and b) a splint oligonucleotide comprising a target sequence and a probe sequence complement, wherein said target sequence is substantially identical to a sequence in said target polynucleotide, and wherein said probe sequence complement is capable of hybridizing to said probe sequence of said oligonucleotide probe.

[0394] Embodiment P33. The kit of Embodiment P32, further comprising a ligase and one or more polymerases.

[0395] Embodiment P34. The kit of Embodiment P33, wherein said one or more polymerases comprise a reverse transcriptase.

[0396] Embodiment P35. The kit of any one of Embodiments P32 to P34, further comprising an exonuclease, wherein said exonuclease is capable of removing a single-stranded nucleic acid sequence.

[0397] Embodiment 1. A method of sequencing in a cell or tissue, said method comprising: contacting a cell or tissue with a probe oligonucleotide and binding an RNA binding sequence of the probe oligonucleotide to an RNA molecule, wherein said probe oligonucleotide further comprises a splint binding sequence; extending the RNA binding sequence along the RNA molecule to form a complementary sequence comprising a first target sequence and a second target sequence; contacting the cell or tissue with a splint oligonucleotide and binding a first sequence of the splint oligonucleotide to the splint binding sequence and binding a second sequence of the splint oligonucleotide to the second target sequence; forming a circular polynucleotide comprising the first sequence, or a complement thereof, and the second sequence, or a complement thereof, amplifying the circular polynucleotide to generate an amplification product comprising multiple copies of the first sequence, or a complement thereof, and the second sequence, or a complement thereof; and sequencing the amplification product.

[0398] Embodiment 2. The method of Embodiment 1, wherein forming the circular polynucleotide comprises ligating a first end and a second end of the probe oligonucleotide together.

[0399] Embodiment 3. The method of Embodiment 1, wherein forming the circular oligonucleotide comprises contacting the complementary sequence with an exonuclease enzyme and generating a 3’ end, wherein said exonuclease enzyme removes a portion of said second target sequence, and ligating a 3 ’ end and splint binding sequence together.

[0400] Embodiment 4. The method of Embodiment 1, wherein forming the circular polynucleotide comprises extending the splint oligonucleotide along the complementary sequence to form a complement of the first sequence and a complement of the second sequence, and ligating a first end and a second end of the splint oligonucleotide together.

[0401] Embodiment 5. The method of any one of Embodiments 1 to 4, wherein prior to contacting the cell or tissue with a splint oligonucleotide, the probe oligonucleotide comprises from 5’ to 3’, the splint binding sequence, the RNA binding sequence, the first target sequence, and the second target sequence.

[0402] Embodiment 6. The method of any one of Embodiments 1 to 5, wherein amplifying the circular polynucleotide comprises hybridizing a primer to said circular polynucleotide and extending said primer with a strand-displacing polymerase.

[0403] Embodiment 7. The method of any one of Embodiments 1 to 5, wherein amplifying comprises incubating the circular polynucleotide with a strand-displacing polymerase for about 15 minutes to about 2 hours.

[0404] Embodiment 8. The method of any one of Embodiments 1 to 5, wherein amplifying comprises incubating the circular polynucleotide with a strand-displacing polymerase for about 30 minutes to about 60 minutes.

[0405] Embodiment 9. The method of any one of Embodiments 1 to 8, wherein the probe oligonucleotide further comprises a primer binding sequence.

[0406] Embodiment 10. The method of Embodiment 9, wherein amplifying comprises binding an amplification primer to the primer binding sequence and extending the amplification primer with a strand-displacing polymerase. [0407] Embodiment 11. The method of any one of Embodiments 1 to 10, prior to contacting the cell or tissue with a splint oligonucleotide, the method comprises removing said RNA molecule.

[0408] Embodiment 12. The method of Embodiment 11, wherein removing said RNA molecule comprises contacting said RNA molecule with a ribonuclease.

[0409] Embodiment 13. The method of any one of Embodiments 1 to 12, wherein sequencing comprises sequencing by synthesis, sequencing by binding, or sequencing by ligation.

[0410] Embodiment 14. The method of any one of Embodiments 1 to 12, wherein sequencing comprises extending a sequencing primer by incorporating a labeled nucleotide or labeled nucleotide analogue, and detecting the label to generate a signal for each incorporated nucleotide or nucleotide analogue, wherein the sequencing primer is hybridized to the amplification product.

[0411] Embodiment 15. The method of any one of Embodiments 1 to 14, wherein said cell is permeabilized and immobilized to a solid support.

[0412] Embodiment 16. A method of generating a complex comprising a circular polynucleotide in a cell, said method comprising: a) hybridizing a splint oligonucleotide to an extended oligonucleotide probe, thereby forming a complex, wherein said splint oligonucleotide comprises a probe sequence complement and a target sequence, wherein said probe sequence complement of said splint oligonucleotide hybridizes to a probe sequence of said extended oligonucleotide probe, wherein said target sequence of said splint oligonucleotide hybridizes to a target sequence complement of said extended oligonucleotide probe, and wherein a subject sequence complement is located between said probe sequence and said target sequence complement of said extended oligonucleotide probe; b) contacting the complex with an exonuclease enzyme and generating an extended oligonucleotide probe comprising a 3’ end, wherein said exonuclease enzyme removes a single-stranded portion of the complex; and c) ligating the probe sequence to the 3’ end of the extended oligonucleotide probe, thereby generating a complex comprising a circular oligonucleotide.

[0413] Embodiment 17. The method of Embodiment 16, wherein prior to step a) the method further comprises hybridizing an oligonucleotide probe to a target polynucleotide in a cell, said target polynucleotide comprising, from 5’ to 3’, said target sequence said subject sequence, and a probe hybridization sequence, wherein said probe hybridization sequence is complementary to a 3’ end of said oligonucleotide probe, and extending said oligonucleotide probe along said target polynucleotide with a polymerase to generate said extended oligonucleotide probe.

[0414] Embodiment 18. The method of Embodiment 16 or 17, further comprising amplifying the circular polynucleotide, thereby generating an amplification product comprising multiple copies of said subject sequence.

[0415] Embodiment 19. A complex comprising: i) a circular polynucleotide comprising a probe sequence, a target hybridization sequence, a subject sequence complement, and a target sequence complement; and ii)a splint oligonucleotide hybridized to said circular polynucleotide, wherein said splint oligonucleotide comprises a probe sequence complement hybridized to said probe sequence of said circular polynucleotide, and wherein said splint oligonucleotide comprises a target sequence hybridized to said target sequence complement of said circular polynucleotide.

[0416] Embodiment 20. The complex of Embodiment 19, wherein said circular polynucleotide further comprises a single-stranded sequence at a 3’ end.

[0417] Embodiment 21. The complex of Embodiment 19 or 20, wherein said splint oligonucleotide further comprises a spacer sequence between said target sequence and said probe sequence complement.

[0418] Embodiment 22. The complex of any one of Embodiments 19 to 21, wherein said probe sequence of said circular polynucleotide comprises one or more primer binding sequences.

[0419] Embodiment 23. The complex of any one of Embodiments 19 to 22, wherein said subject sequence complement of said circular polynucleotide comprises a sequencing primer binding sequence.

[0420] Embodiment 24. A kit comprising: a) an oligonucleotide probe comprising a target hybridization sequence and a probe sequence, wherein said target hybridization sequence is complementary to a probe hybridization sequence in a target polynucleotide; and b) a splint oligonucleotide comprising a target sequence and a probe sequence complement, wherein said target sequence is substantially identical to a sequence in said target polynucleotide, and wherein said probe sequence complement is capable of hybridizing to said probe sequence of said oligonucleotide probe.

[0421] Embodiment 25. The kit of Embodiment 24, further comprising a ligase and one or more polymerases. [0422] Embodiment 26. The kit of Embodiment 25, wherein said one or more polymerases comprise a reverse transcriptase.

[0423] Embodiment 27. The kit of any one of Embodiments 24 to 26, further comprising an exonuclease, wherein said exonuclease is capable of removing a single-stranded nucleic acid sequence.

[0424] Embodiment 28. A cell comprising the complex of any one of claims 19 to 23.

Claims

WHAT IS CLAIMED IS:

1. A method of sequencing in a cell or tissue, said method comprising: contacting a cell or tissue with a probe oligonucleotide and binding an RNA binding sequence of the probe oligonucleotide to an RNA molecule, wherein said probe oligonucleotide further comprises a splint binding sequence; extending the RNA binding sequence along the RNA molecule to form a complementary sequence comprising a first target sequence and a second target sequence; contacting the cell or tissue with a splint oligonucleotide and binding a first sequence of the splint oligonucleotide to the splint binding sequence and binding a second sequence of the splint oligonucleotide to the second target sequence; forming a circular polynucleotide comprising the first sequence, or a complement thereof, and the second sequence, or a complement thereof, amplifying the circular polynucleotide to generate an amplification product comprising multiple copies of the first sequence, or a complement thereof, and the second sequence, or a complement thereof; and sequencing the amplification product.

2. The method of claim 1, wherein forming the circular polynucleotide comprises ligating a first end and a second end of the probe oligonucleotide together.

3. The method of claim 1, wherein forming the circular oligonucleotide comprises contacting the complementary sequence with an exonuclease enzyme and generating a 3’ end, wherein said exonuclease enzyme removes a portion of said second target sequence, and ligating a 3 ’ end and splint binding sequence together.

4. The method of claim 1, wherein forming the circular polynucleotide comprises extending the splint oligonucleotide along the complementary sequence to form a complement of the first sequence and a complement of the second sequence, and ligating a first end and a second end of the splint oligonucleotide together.

5. The method of claim 1, wherein prior to contacting the cell or tissue with a splint oligonucleotide, the probe oligonucleotide comprises from 5’ to 3’, the splint binding sequence, the RNA binding sequence, the first target sequence, and the second target sequence.

6. The method of claim 1, wherein amplifying the circular polynucleotide comprises hybridizing a primer to said circular polynucleotide and extending said primer with a strand-displacing polymerase.

7. The method of claim 1, wherein amplifying comprises incubating the circular polynucleotide with a strand-displacing polymerase for about 15 minutes to about 2 hours.

8. The method of claim 1, wherein amplifying comprises incubating the circular polynucleotide with a strand-displacing polymerase for about 30 minutes to about 60 minutes.

9. The method of claim 1, wherein the probe oligonucleotide further comprises a primer binding sequence.

10. The method of claim 9, wherein amplifying comprises binding an amplification primer to the primer binding sequence and extending the amplification primer with a strand-displacing polymerase.

11. The method of claim 1, prior to contacting the cell or tissue with a splint oligonucleotide, the method comprises removing said RNA molecule.

12. The method of claim 11, wherein removing said RNA molecule comprises contacting said RNA molecule with a ribonuclease.

13. The method of claim 1, wherein sequencing comprises sequencing by synthesis, sequencing by binding, or sequencing by ligation.

14. The method of claim 1, wherein sequencing comprises extending a sequencing primer by incorporating a labeled nucleotide or labeled nucleotide analogue, and detecting the label to generate a signal for each incorporated nucleotide or nucleotide analogue, wherein the sequencing primer is hybridized to the amplification product.

15. The method of claim 1, wherein said cell is permeabilized and immobilized to a solid support.

16. A method of generating a complex comprising a circular polynucleotide in a cell, said method comprising: a) hybridizing a splint oligonucleotide to an extended oligonucleotide probe, thereby forming a complex, wherein said splint oligonucleotide comprises a probe sequence complement and a target sequence, wherein said probe sequence complement of said splint oligonucleotide hybridizes to a probe sequence of said extended oligonucleotide probe, wherein said target sequence of said splint oligonucleotide hybridizes to a target sequence complement of said extended oligonucleotide probe, and wherein a subject sequence complement is located between said probe sequence and said target sequence complement of said extended oligonucleotide probe; b) contacting the complex with an exonuclease enzyme and generating an extended oligonucleotide probe comprising a 3’ end, wherein said exonuclease enzyme removes a singlestranded portion of the complex; and c) ligating the probe sequence to the 3’ end of the extended oligonucleotide probe, thereby generating a complex comprising a circular oligonucleotide.

17. The method of claim 16, wherein prior to step a) the method further comprises hybridizing an oligonucleotide probe to a target polynucleotide in a cell, said target polynucleotide comprising, from 5’ to 3’, said target sequence said subject sequence, and a probe hybridization sequence, wherein said probe hybridization sequence is complementary to a 3’ end of said oligonucleotide probe, and extending said oligonucleotide probe along said target polynucleotide with a polymerase to generate said extended oligonucleotide probe.

18. The method of claim 16, further comprising amplifying the circular polynucleotide, thereby generating an amplification product comprising multiple copies of said subject sequence.

19. A complex comprising: i) a circular polynucleotide comprising a probe sequence, a target hybridization sequence, a subject sequence complement, and a target sequence complement; and ii) a splint oligonucleotide hybridized to said circular polynucleotide, wherein said splint oligonucleotide comprises a probe sequence complement hybridized to said probe sequence of said circular polynucleotide, and wherein said splint oligonucleotide comprises a target sequence hybridized to said target sequence complement of said circular polynucleotide.

20. The complex of claim 19, wherein said circular polynucleotide further comprises a single-stranded sequence at a 3’ end.

21. The complex of claim 19, wherein said splint oligonucleotide further comprises a spacer sequence between said target sequence and said probe sequence complement.

22. The complex of claim 19, wherein said probe sequence of said circular polynucleotide comprises one or more primer binding sequences.

23. The complex of claim 19, wherein said subject sequence complement of said circular polynucleotide comprises a sequencing primer binding sequence.

24. A kit comprising: a) an oligonucleotide probe comprising a target hybridization sequence and a probe sequence, wherein said target hybridization sequence is complementary to a probe hybridization sequence in a target polynucleotide; and b) a splint oligonucleotide comprising a target sequence and a probe sequence complement, wherein said target sequence is substantially identical to a sequence in said target polynucleotide, and wherein said probe sequence complement is capable of hybridizing to said probe sequence of said oligonucleotide probe.

25. The kit of claim 24, further comprising a ligase and one or more polymerases.

26. The kit of claim 25, wherein said one or more polymerases comprise a reverse transcriptase.

27. The kit of claim 24, further comprising an exonuclease, wherein said exonuclease is capable of removing a single-stranded nucleic acid sequence.

28. A cell comprising the complex of claim 20.