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| Status |
Public on Sep 01, 2021 |
| Title |
Gene expression profiling of late reprogramming stages during in vitro reprogramming of mouse embryonic fibroblasts (MEFs) to induced pluripotent stem cells (iPSCs) |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The generation of induced pluripotent stem cells (iPSCs) involves activation of the endogenous pluripotency circuitry and global DNA demethylation late in reprogramming, but temporal resolution of these events are insufficient using existing stage markers. Here, we generated murine transgenic lines harboring dual fluorescent reporters reflecting cell-state specific expression of the master pluripotency factor Oct4 and the 5-methylcytosine dioxygenase Tet1. By assessing reprogramming intermediates based on dual reporter patterns, we identified a sequential order of Tet1 and Oct4 gene activation at proximal and distal regulatory elements following pluripotency entry. A transient phase of global gene repression accompanies full activation of Tet1, precedes activation of meiotic and gametogenesis genes, and distinguishes phases of global DNA demethylation reminiscent of germ-line reprogramming. Loss of Tet1 is compatible with reprogramming towards full Oct4 gene activation, but generates iPSCs with epigenetic defects. Therefore, the transcriptional logic of Tet1 expression signals an epigenetic roadmap towards efficient reprogramming.
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| Overall design |
Transcriptome analysis of parental MEF, late reprogramming intermediate stages and clonally expanded wild type and TET1 knockout (KO) iPSCs all in biological triplicates by RNA-seq.
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| Contributor(s) |
Bartoccetti M, Luo X, Koh K |
| Citation(s) |
32075734 |
| |
| Submission date |
Sep 11, 2018 |
| Last update date |
Sep 01, 2021 |
| Contact name |
Kian Peng Koh |
| E-mail(s) |
kian.koh@kuleuven.be
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| Organization name |
KULeuven
|
| Street address |
Herestraat 49, O&N IV - box 804
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| City |
Leuven |
| State/province |
Select... |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (42)
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| This SubSeries is part of SuperSeries: |
| GSE119831 |
Dynamics of Tet1 and Oct4 gene activation identify temporally distinct late stages in reprogramming of induced pluripotency |
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| Relations |
| BioProject |
PRJNA490383 |
| SRA |
SRP161523 |
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