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| Status |
Public on Jul 27, 2018 |
| Title |
Novel Principles of Cellular Reprogramming Revealed by Prospective Isolation and Characterization of Rare Intermediates Poised to Generate iPSCs [RNA-seq 1] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Cellular reprogramming converts differentiated cells into induced pluripotent stem cells (iPSCs). However, this process is extremely inefficient, complicating mechanistic studies. Here, we identified and molecularly characterized rare, early intermediates poised to reprogram with up to 100% efficiency, without perturbing additional genes or pathways. Analysis of these cells uncovered transcription factors (e.g., Tfap2c, Bex2), which are critical for reprogramming but dispensable for pluripotency maintenance. Additionally, we observed striking patterns of chromatin hyperaccessibility at pluripotency loci, which preceded gene expression in poised intermediates. Finally, inspection of these hyperaccessible regions revealed a previously unappreciated early wave of DNA demethylation, which is uncoupled from de novo methylation of somatic regions late in reprogramming. Overall, our study underscores the importance of investigating the rare intermediates poised to produce iPSCs, provides novel insights into the mechanisms of reprogramming, and offers a valuable resource for the dissection of transcriptional and epigenetic dynamics intrinsic to cell fate change.
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| Overall design |
RNA-seq of reprogramming intermediates (11 cell types in triplicate).
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| Contributor(s) |
Schwarz BA, Cetinbas M, Clement K, Walsh RM, Cheloufi S, Gu H, Meissner A, Sadreyev R, Hochedlinger K |
| Citation(s) |
30017590 |
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| Submission date |
Nov 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Benjamin A Schwarz |
| Organization name |
MGH
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| Department |
Molecular Biology
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| Lab |
Hochedlinger
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| Street address |
185 Cambridge St.
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (33)
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| GSM2855063 |
d3 SSEA1-, replicate1, RNA-seq |
| GSM2855064 |
d3 SSEA1-, replicate2, RNA-seq |
| GSM2855065 |
d3 SSEA1-, replicate3, RNA-seq |
| GSM2855066 |
d6 SSEA1-, replicate1, RNA-seq |
| GSM2855067 |
d6 SSEA1-, replicate2, RNA-seq |
| GSM2855068 |
d6 SSEA1-, replicate3, RNA-seq |
| GSM2855069 |
d9 SSEA1-, replicate1, RNA-seq |
| GSM2855070 |
d9 SSEA1-, replicate2, RNA-seq |
| GSM2855071 |
d9 SSEA1-, replicate3, RNA-seq |
| GSM2855072 |
d12 SSEA1-, replicate1, RNA-seq |
| GSM2855073 |
d12 SSEA1-, replicate2, RNA-seq |
| GSM2855074 |
d12 SSEA1-, replicate3, RNA-seq |
| GSM2855075 |
iPS SSEA1-, replicate1, RNA-seq |
| GSM2855076 |
iPS SSEA1-, replicate2, RNA-seq |
| GSM2855077 |
iPS SSEA1-, replicate3, RNA-seq |
| GSM2855078 |
d3 SSEA1+, replicate1, RNA-seq |
| GSM2855079 |
d3 SSEA1+, replicate2, RNA-seq |
| GSM2855080 |
d3 SSEA1+, replicate3, RNA-seq |
| GSM2855081 |
d6 SSEA1+, replicate1, RNA-seq |
| GSM2855082 |
d6 SSEA1+, replicate2, RNA-seq |
| GSM2855083 |
d6 SSEA1+, replicate3, RNA-seq |
| GSM2855084 |
d9 SSEA1+, replicate1, RNA-seq |
| GSM2855085 |
d9 SSEA1+, replicate2, RNA-seq |
| GSM2855086 |
d9 SSEA1+, replicate3, RNA-seq |
| GSM2855087 |
d12 SSEA1+, replicate1, RNA-seq |
| GSM2855088 |
d12 SSEA1+, replicate2, RNA-seq |
| GSM2855089 |
d12 SSEA1+, replicate3, RNA-seq |
| GSM2855090 |
iPS SSEA1+, replicate1, RNA-seq |
| GSM2855091 |
iPS SSEA1+, replicate2, RNA-seq |
| GSM2855092 |
iPS SSEA1+, replicate3, RNA-seq |
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| This SubSeries is part of SuperSeries: |
| GSE106838 |
Novel Principles of Cellular Reprogramming Revealed by Prospective Isolation and Characterization of Rare Intermediates Poised to Generate iPSCs |
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| Relations |
| BioProject |
PRJNA418162 |
| SRA |
SRP124865 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE106835_RAW.tar |
4.6 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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