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| Status |
Public on Apr 17, 2011 |
| Title |
Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Human induced pluripotent stem (iPS) cells are remarkably similar to embryonic stem (ES) cells, but recent reports indicate that there may be important differences between them. We carried out a systematic comparison of human iPS cells generated from hepatocytes (representative of endoderm), skin fibroblasts (mesoderm) and melanocytes (ectoderm). All low-passage iPS cells analysed retain a transcriptional memory of the original cells. The persistent expression of somatic genes can be partially explained by incomplete promoter DNA methylation. This epigenetic mechanism underlies a robust form of memory that can be found in iPS cells generated by multiple laboratories using different methods, including RNA transfection. Incompletely silenced genes tend to be isolated from other genes that are repressed during reprogramming, indicating that recruitment of the silencing machinery may be inefficient at isolated genes. Knockdown of the incompletely reprogrammed gene C9orf64 (chromosome 9 open reading frame 64) reduces the efficiency of human iPS cell generation, indicating that somatic memory genes may be functionally relevant during reprogramming.
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| Overall design |
iPS cells were produced from melanocytes, fibroblasts, and hepatocytes, representing the three germ layers. Expression levels were profiled in the differentiated cells and their matched iPS cells, as well as 3 human ES cell lines (H1, H7 and H9) and their embroid bodies.
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| Contributor(s) |
Ohi Y, Qin H, Hong C, Blouin L, Polo JM, Guo T, Qi Z, Downey SL, Manos PD, Rossi DJ, Yu J, Hebrok M, Hochedlinger K, Costello JF, Song JS, Ramalho-Santos M |
| Citation(s) |
21499256 |
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| Submission date |
Jul 20, 2010 |
| Last update date |
Mar 22, 2012 |
| Contact name |
Jun S Song |
| Organization name |
UCSF
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| Department |
Institute for Human Genetics
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| Street address |
513 Parnassus Avenue, Box 0794
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143-0794 |
| Country |
USA |
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| Platforms (1) |
| GPL10666 |
Affymetrix Human Gene ST 1.0 Custom RefSeq CDF version 12 [CDF: HuGene10stv1_Hs_REFSEQ] |
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| Samples (24)
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| GSM568484 |
Hepatocyte-iPS, Rep 1 |
| GSM568485 |
Hepatocyte-iPS, Rep 2 |
| GSM568486 |
Hepatocyte-iPS, Rep 3 |
| GSM568487 |
Fibroblast, Rep 1 |
| GSM568488 |
Fibroblast, Rep 2 |
| GSM568489 |
Fibroblast, Rep 3 |
| GSM568490 |
Fibroblast-iPS, Rep 1 |
| GSM568491 |
Fibroblast-iPS, Rep 2 |
| GSM568492 |
Fibroblast-iPS, Rep 3 |
| GSM568493 |
Melanocyte, Rep 1 |
| GSM568494 |
Melanocyte, Rep 2 |
| GSM568495 |
Melanocyte, Rep 3 |
| GSM568496 |
Melanocyte-iPS, Rep 1 |
| GSM568497 |
Melanocyte-iPS, Rep 2 |
| GSM568498 |
Melanocyte-iPS, Rep 3 |
| GSM568499 |
H1 |
| GSM568500 |
H7 |
| GSM568501 |
H9 |
| GSM568502 |
H1-EB |
| GSM568503 |
H7-EB |
| GSM568504 |
H9-EB |
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| Relations |
| BioProject |
PRJNA131167 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE23034_RAW.tar |
111.1 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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