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| Status |
Public on Apr 27, 2009 |
| Title |
Digital DNA methylation analysis of stem cell reprogramming by targeted bisulfite sequencing |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
We report a method for specific capture of an arbitrary subset of genomic targets for single molecule bisulfite sequencing, and for digital quantitation of DNA methylation at a single nucleotide resolution. We used targeted bisulfite sequencing to characterize the changes of DNA methylation during the de-differentiation of human fibroblasts into hybrid stem cells, and into induced pluripotent stem cells. We compared the methylation level of approximately 66,000 CpG sites within 2020 CpG islands on chromosome 12, chromosome 20, and 34 selected regions. A total of 288 differentially methylated regions were identified between fibroblasts and pluripotent cells. Methylation cluster analysis revealed distinct methylation patterns between fibroblasts and pluripotent cells. Furthermore iPS cells are globally more methylated than human embryonic stem cells, which could be due to the reprogramming process. This targeted bisulfite sequencing method is particularly useful for efficient and large-scale analysis of DNA methylation in organisms with large genomes.
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| Overall design |
Comparison of DNA methylation on 2020 CpG islands and 34 other selected regions among eleven human ES, iPS and fibroblast lines.
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| Contributor(s) |
Zhang K |
| Citation(s) |
19330000 |
| |
| Submission date |
Feb 25, 2009 |
| Last update date |
Mar 21, 2012 |
| Contact name |
Kun Zhang |
| E-mail(s) |
kzhang@bioeng.ucsd.edu
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| Phone |
8588227876
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| Organization name |
University of California at San Diego
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| Department |
Bioengineering
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| Street address |
9500 Gilman Drive, MC0412
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platforms (1) |
| GPL8230 |
UCSD-CpgMIP-targeted-bisulfite-sequencing |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA114721 |