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Series GSE41361 Query DataSets for GSE41361
Status Public on Jun 24, 2013
Title Role for DNA methylation in Gata4-binding in embryonic stem cells-derived mesoderm
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary During embryogenesis, many key transcription factors are used repeatedly, achieving different outcomes depending on cell type and developmental stage. The epigenetic modification of the genome functions as a memory of a cell’s developmental history, and it has been proposed that such modification shapes the cellular response to transcription factors. To investigate the role of DNA methylation in the response to transcription factor Gata4, we have tried to identify GATA4-binding associated genes of WT-type and Dnmt3a-/-Dnmt3b-/-(DKO) in Flk1-based mesoderm progenitor by Gata4 ChIP-analysis.
Overall design Wild-type and DKO ES cell clones stably expressing dexamethasone (Dex)-inducible Gata4 were generated by introducing an expression plasmid for Gata4 fused with the ligand-binding domain of the human glucocorticoid receptor (Gata4GR) driven by the CAG promoter, by electroporation. For mesoderm differentiation, 5.4 x 10^5 ES for WT, 6.5 x 10^5 ES cells for DKO, were plated onto OP9 stroma-culture in 15-cm dish. Day. 4.5-differentiated cells were treated with 100 nM Dex for 3 hours and then collected as single-cell suspensions using 0.25% trypsin-EDTA, followed by incubation in differentiation medium at 37˚C to allow cell-surface markers to recover. Flk1(+) cells were sorted by AutoMACS (Miltenyi Biotec) and crosslinked with 1% formaldehyde for Gata4 ChIP-seq analysis.
Contributor(s) Shigeta M, Niwa H
Citation(s) 23825962
Submission date Oct 05, 2012
Last update date May 15, 2019
Contact name Masaki Shigeta
Organization name Kyoto prefectural university of medicine
Department Department of Anatomy and Developmental Biology
Street address 465 Kajii-cho, Kawaramachi-street, Hitokojiagaru, Kamigyo-ku
City Kyoto
State/province Kyoto
ZIP/Postal code 602-8566
Country Japan
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (4)
GSM1015512 Flk1+Dex+Wild-type_ChIPSeq
GSM1015513 Flk1+Dex+DKO_ChIPSeq
GSM1015514 ES_Dex-_Wild-type_ChIPSeq
BioProject PRJNA176686
SRA SRP016005

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

Supplementary file Size Download File type/resource
GSE41361_Flk1_DKO_GATA-4.peaks.txt.gz 4.5 Mb (ftp)(http) TXT
GSE41361_Flk1_wild-type_GATA-4.peaks.txt.gz 4.0 Mb (ftp)(http) TXT
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Processed data are available on Series record

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