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Series GSE96661 Query DataSets for GSE96661
Status Public on May 15, 2017
Title Chd2 knockout effect on chromatin remodelling and the expression of developmental genes in mouse embryonic stem cells (RNA-Seq)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary We demonstrate that chromodomain helicase DNA-binding domain 2 (Chd2) is required to maintain the differentiation potential of mouse ESCs. Chd2-depleted ESCs showed suppressed expression of developmentally regulated genes upon differentiation and subsequent differentiation defects without affecting gene expression in the undifferentiated state. Furthermore, chromatin immunoprecipitation followed by sequencing revealed alterations in a proportion of nucleosomes of developmentally regulated genes in Chd2-depleted ESCs to enhance histone variant H3.3 enrichment, leading to elevated trimethylation of histone H3 lysine 27.Chd2 is essential to prevent suppressive chromatin formation in developmentally regulated genes and determines subsequent effects on developmental processes in the undifferentiated state.
 
Overall design Evaluation of three histone modifications, H3.3 and total H3 in WT and Chd2mut/mut mESCs (ChIP-Seq), and of mRNA expression (RNA-Seq).
 
Contributor(s) Ohkawa Y, Semba Y, Harada A, Maehara K, Nogami J
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Submission date Mar 15, 2017
Last update date May 15, 2019
Contact name Yasuyuki Ohkawa
E-mail(s) yohkawa@bioreg.kyushu-u.ac.jp
Organization name Medical Institute of Bioregulation
Lab Division of Transcriptomics
Street address 3-1-1 Maidashi
City Fukuoka
ZIP/Postal code 8128582
Country Japan
 
Platforms (1)
GPL15103 Illumina HiSeq 1000 (Mus musculus)
Samples (4)
GSM2537654 WT_RNAseq_lot1
GSM2537655 WT_RNAseq_lot2
GSM2537656 Chd2KO_RNAseq_lot1
This SubSeries is part of SuperSeries:
GSE96662 Chd2 knockout effect on chromatin remodelling and the expression of developmental genes in mouse embryonic stem cells
Relations
BioProject PRJNA379311
SRA SRP101962

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

Supplementary file Size Download File type/resource
GSE96661_FPKM_matrix.txt.gz 307.1 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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