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| Status |
Public on Jul 22, 2020 |
| Title |
Role of the histone demethylase Kdm6b/Jmjd3 in somatic cell reprogramming [ATAC-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Somatic cells can be reprogrammed to pluripotent stem cells through the addition of just four transcription factors, OCT4, SOX2, KLF4 and c-MYC (OSKM). Although OSKM initiates reprogramming it is clear that extensive epigenetic remodeling is required to complete reprogramming. Critically, OSKM do not directly activate gene expression but instead recruit co-activators and co-repressors that remodel the local chromatin and in some way make the cells permissive for reprogramming. Consequently understanding how epigenetic co-repressors and co-activators are involved in reprogramming is a critical step in understanding the reprogramming process in detail. In this study we explored the role of the lysine-specific demethylase Kdm6b/Jmjd3 and its role in the reprogramming of somatic cells to pluripotent cells.
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| Overall design |
ChIP-seq data consists of either input chromatin (MEF cells) or anti-H3K27me3 precipitated chromatin. Experiments were performed at three time points (MEFS, Day 5 and 10 of reprogramming cells) and in two MEF lines, one with Jmjd3wildtype and another with Jmjd3 Knockout. Additionally, either FLAG or Jmjd3 was overexpressed. The Jmjd3 knockout mice were a kind gift from Dr. Takashi Satoh (Takashi et al., 2010 Nat. Immunol.). ATAC-seq data was performed according to Buenrostro et al., 2015, on MEFs, ESCs, and Day 5 and day 10 OSKM-reprogramming cells
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| Contributor(s) |
Hutchins AP, Qin B, Yinghua H |
| Citation(s) |
33033262 |
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| Submission date |
Apr 28, 2020 |
| Last update date |
Oct 21, 2020 |
| Contact name |
Andrew P Hutchins |
| E-mail(s) |
andrewh@sustech.edu.cn
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| Organization name |
Southern University of Science and Technology
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| Department |
Bioinformatics
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| Lab |
Bioinformatics and Genomics
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| Street address |
1088 Xueyuan Rd
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| City |
Shenzhen |
| ZIP/Postal code |
518055 |
| Country |
China |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE75005 |
Role of the histone demethylase Kdm6b/Jmjd3 in somatic cell reprogramming |
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| Relations |
| BioProject |
PRJNA628934 |
| SRA |
SRP258905 |
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