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Series GSE19461 Query DataSets for GSE19461
Status Public on Nov 11, 2011
Title Activin/Nodal signalling controls divergent transcriptional networks in pluripotent and endoderm progenitors.
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Activin/Nodal signalling is necessary to maintain pluripotency of human Embryonic Stem Cells (hESCs) and to induce their differentiation towards endoderm. However, the mechanisms by which Activin/Nodal signalling achieves these opposite functions remain unclear. To unravel these mechanisms, we examined the transcriptional network controlled in hESCs by Smad2 and Smad3 which represent the direct effectors of Activin/Nodal signalling. These analyses reveal that Smad2/3 participate in the control of the core transcriptional network characterising pluripotency which includes Oct-4, Nanog, FoxD3, Dppa4, Tert, Myc and UTF-1. In addition, similar experiments performed on endoderm cells confirm that a broad part of the transcriptional network directing differentiation is downstream of Smad2/3. Therefore, Activin/Nodal signalling appears to control divergent transcriptional networks in hESCs and in endoderm. Importantly, we observed an overlap between the transcriptional network downstream of Nanog and Smad2/3 in hESCs while functional studies showed that both factors cooperate to control the expression of pluripotency genes. Therefore, the effect of Activin/Nodal signalling on pluripotency and differentiation could be dictated by tissue specific Smad2/3 partners such as Nanog, explaining the mechanisms by which signalling pathways can orchestrate divergent cell fate decisions.
Overall design Identification of Smad2/3 binding sites in pluripotent hESCs. 5 ChIP-Seq samples including 1 input control sample and 4 ChIP samples (two conditions x two replicates).
Contributor(s) Vallier L, Brown S, Trotter M
Citation(s) 21630377
Submission date Dec 14, 2009
Last update date May 15, 2019
Contact name Matthew Trotter
Organization name University of Cambridge
Department Department of Surgery
Lab Laboratory for Regenerative Medicine
Street address West Forvie Building, Forvie Site, Robinson Way
City Cambridge
ZIP/Postal code CB2 0SZ
Country United Kingdom
Platforms (1)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Samples (5)
GSM761754 hESC_Input_XL
GSM761755 hESC_D0_Smad_XL_rep1
GSM761756 hESC_D0_Smad_XL_rep2
SRA SRP002216
BioProject PRJNA120331

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Supplementary file Size Download File type/resource
GSE19461_RAW.tar 3.7 Gb (http)(custom) TAR (of BED, TXT)
GSE19461_README.txt 1.6 Kb (ftp)(http) TXT
GSE19461_SMAD_XL_D0_BothReps_2M_RM.bed.gz 140.6 Mb (ftp)(http) BED
GSE19461_SMAD_XL_D0_BoundRegions.gff.gz 119.4 Kb (ftp)(http) GFF
GSE19461_SMAD_XL_D3_BothReps_2M_RM.bed.gz 150.6 Mb (ftp)(http) BED
GSE19461_SMAD_XL_D3_BoundRegions.gff.gz 130.7 Kb (ftp)(http) GFF
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Processed data provided as supplementary file
Raw data are available in SRA
Processed data are available on Series record

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