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Series GSE18507 Query DataSets for GSE18507
Status Public on Feb 09, 2010
Title Transcriptional Networks in Mouse Trophoblast Stem Cell Self-Renewal
Organism Mus musculus
Experiment type Expression profiling by array
Genome binding/occupancy profiling by genome tiling array
Summary Trophoblast stem cells (TS cells), derived from the trophectoderm (TE) of blastocysts, require transcription factors (TFs) and external signals (Fgf4, Activin/Nodal/Tgfb) for self-renewal. While many reports have focused on TF networks that regulate embryonic stem cell (ES cell) self-renewal and pluripotency, little is know about TF networks that regulate self-renewal in TS cells. To further understand transcriptional networks in TS cells we used chromatin immunopreciptiation and DNA microarray analysis (ChIP-chip) to investigate targets of TFs Ap-2g (Tcfap2c), Eomes, Ets2, and Gata3, and a chromatin remodeling factor, Brg1 (Smarca4). We then evaluated the transcriptional states of target genes using transcriptome analysis and genome-wide analysis of histone H3 acetylation (AcH3). Our results describe previously unknown transcriptional networks in TS cells, including TF occupancy of genes involved in ES cell self-renewal and pluripotency, co-occupancy of multiple TFs at target genes, and transcriptional regulatory circuitry within the 5 factors. Through genome-wide mapping and global expression analysis of 5 TF target genes, our data provide a comprehensive analysis of transcriptional networks that regulate TS cell self-renewal.
 
Overall design RNA was harvested at 7 time points from TS cells cultured without Fgf4 over two weeks for transcriptome analysis. RNA was collected from undifferentiated TS cells at T=0hr, and differentiated TS cells cultured without Fgf4 for 24-hrs, 48-hrs, 72-hrs, 6 days, 10 days, and 14 days.

Mouse TS cells were ChIPed with antibodies specific to Ap-2g (Tcfap2c), Brg1 (Smarca4), Eomes, Ets2, and Gata3 vs. Input DNA from TS cells
 
Contributor(s) Kidder BL
Citation(s) 20176728
Submission date Oct 09, 2009
Last update date Feb 11, 2019
Contact name Benjamin L Kidder
Organization name EMD Serono Research Institute
Department Reproductive Health
Street address 1 Technology Place
City Rockland
State/province MA
ZIP/Postal code 02370
Country USA
 
Platforms (2)
GPL1261 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
GPL5811 [Mm_PromPR] Affymetrix Mouse Promoter 1.0R Array
Samples (19)
GSM461162 TS cell, 0hr, rep1
GSM461163 TS cell, 0hr, rep2
GSM461164 TS cell, 24hr, rep1
Relations
BioProject PRJNA118267

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
GSE18507_RAW.tar 680.7 Mb (http)(custom) TAR (of BAR, CEL)
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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