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| Status |
Public on Jul 22, 2020 |
| Title |
Role of the histone demethylase Kdm6b/Jmjd3 in somatic cell reprogramming [ChIP-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/H3K27ac precipitated chromatin, anti-KLF4 ChIP-seq or anti-FLAG ChIP-seq against a FLAG-JMJD3. Experiments were performed at three time points (MEFS, Day 5 and 10 of reprogramming cells) and in two MEF lines, one with Jmjd3 Wildtype 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.)
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| Contributor(s) |
Hutchins AP, Qin B, Yinghua H |
| Citation(s) |
33033262 |
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| Submission date |
Nov 13, 2015 |
| 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) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (20)
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| GSM1940097 |
MEF Jmjd3+/+ input |
| GSM1940098 |
OSKM Day 10 Jmjd3-/- FLAG overexpression anti-H3K27me3 |
| GSM1940099 |
OSKM Day 10 Jmjd3-/- Jmjd3 overexpression anti-H3K27me3 |
| GSM1940100 |
OSKM Day 10 Jmjd3+/+ FLAG overexpression anti-H3K27me3 |
| GSM1940101 |
OSKM Day 10 Jmjd3+/+ Jmjd3 overexpression anti-H3K27me3 |
| GSM1940102 |
OSKM Day 5 Jmjd3-/- FLAG overexpression anti-H3K27me3 |
| GSM1940103 |
OSKM Day 5 Jmjd3-/- Jmjd3 overexpression anti-H3K27me3 |
| GSM1940104 |
OSKM Day 5 Jmjd3+/+ FLAG overexpression anti-H3K27me3 |
| GSM1940105 |
OSKM Day 5 Jmjd3+/+ Jmjd3 overexpression anti-H3K27me3 |
| GSM3791661 |
OSKM Day 5 Jmjd3+/+ FLAG overexpression Klf4 |
| GSM3791662 |
OSKM Day 5 Jmjd3+/+ Jmjd3 overexpression Klf4 |
| GSM3791663 |
OSKM Day 5 Jmjd3+/+ FLAG overexpression anti-H3K27ac |
| GSM3791664 |
OSKM Day 5 Jmjd3+/+ Jmjd3 overexpression anti-H3K27ac |
| GSM3791665 |
OSKM Day 5 FLAG-JMJD3 overexpression anti-FLAG |
| GSM3791666 |
OSlowKM Day 5 FLAG-JMJD3 overexpression anti-FLAG |
| GSM3791667 |
OSKM Day 5 FLAG-JMJD3 overexpression input |
| GSM3791668 |
OSlowKM Day 5 FLAG-JMJD3 overexpression input |
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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 |
PRJNA302171 |
| SRA |
SRP066184 |
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