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Series GSE47124 Query DataSets for GSE47124
Status Public on Oct 14, 2013
Title Extended self-renewal and accelerated reprogramming in the absence of Kdm5b [RNA-Seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary ES cell pluripotency is thought to be regulated in part by H3K4 methylation. However, it is unclear how H3K4 demethylation contributes to ES cell function and participates in iPS cell reprogramming. Here, we show that KDM5B, which demethylates H3K4, is important for ES cell differentiation, and presents a barrier to the reprogramming process. Depletion of Kdm5b leads to an extension in the self-renewal of ES cells in the absence of LIF. Transcriptome analysis revealed the persistent expression of pluripotency-genes and underexpression of developmental genes during differentiation in the absence of Kdm5b, suggesting that KDM5B plays a key role in cellular fate changes. We also observed accelerated reprogramming of differentiated cells in the absence of Kdm5b, demonstrating that KDM5B is a barrier to the reprogramming process. Expression analysis revealed that mesenchymal master regulators associated with epithelial-to-mesenchymal transition (EMT) are downregulated during reprogramming in the absence of Kdm5b. Moreover, global analysis of H3K4me3/2 revealed that enhancers of fibroblast genes are rapidly deactivated in the absence of Kdm5b, and genes associated with EMT lose H3K4me3/2 during the early reprogramming process. These findings provide functional insight into the role for KDM5B in regulating ES cell differentiation and as a barrier to the reprogramming process.
Overall design RNA-Seq of undifferentiated and embryoid body (EB) differentiated murine shLuc and shKdm5b ES cells
Contributor(s) Kidder BL, Hu G, Zhao K
Citation(s) 24100015
Submission date May 21, 2013
Last update date May 15, 2019
Contact name Benjamin L Kidder
Organization name Wayne State University
Department Oncology
Lab Laboratory of Stem Cell Epigenomics
Street address 4100 John R St
City Detroit
State/province MI
ZIP/Postal code 48201
Country USA
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (12)
GSM1145403 mES_shLuc_ctrl
GSM1145404 mES_shKdm5b
GSM1145405 EB_24h_shLuc_ctrl
This SubSeries is part of SuperSeries:
GSE46893 Extended self-renewal and accelerated reprogramming in the absence of Kdm5b
BioProject PRJNA203695
SRA SRP022933

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE47124_RAW.tar 3.3 Gb (http)(custom) TAR (of BED, BEDGRAPH, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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