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Series GSE48085 Query DataSets for GSE48085
Status Public on Apr 24, 2014
Title Genome-scale analysis in blood progenitor and mast cells reveals how lineage-affiliated transcription factors control distinct regulatory programs [ChIP-Seq/RNA-Seq Experiments]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Despite major advances in the generation of genome-wide binding maps, the mechanisms by which transcription factors (TFs) regulate cell type identity have remained largely obscure. Through comparative analysis of 10 key haematopoietic TFs in both mast cells and blood progenitors, we demonstrate that the largely cell-type specific binding profiles are not opportunistic, but instead contribute to cell-type specific transcriptional control, because (1) mathematical modelling of differential binding of shared TFs can explain differential gene expression, (2) cell-type specific binding is largely mediated through consensus binding sites, and (3) knock-down of blood stem cell regulators Gata2 and Erg in mast cells reveals mast cell specific genes as direct targets. Finally we show that the known mast cell regulators Mitf and c-Fos likely contribute to the global reorganisation of TF binding profiles. Taken together therefore, our study elucidates how key regulatory TFs contribute to transcriptional programmes in several distinct mammalian cell types.
Overall design Comparison of HPC7 cell line (haematopoietic multipotent progenitor) and primary mast cells. 10 key haematopoietic transcription factors and mRNA expression were profiled in both cell types.
Contributor(s) Calero-Nieto FJ, Ng FS, Wilson NK, Hannah R, Diamanti E, Moignard V, Leal-Cervantes AI, Jimenez-Madrid I, Wernisch L, Gottgens B
Citation(s) 24760698
Submission date Jun 19, 2013
Last update date May 15, 2019
Contact name Felicia Ng
Organization name Cambridge Institute for Medical Research
Street address Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road
City Cambridge
ZIP/Postal code CB3 9BB
Country United Kingdom
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (20)
GSM1167572 ChIPseq_Ctcf_HPC7
GSM1167573 ChIPseq_E2A_HPC7
GSM1167574 ChIPseq_Ctcf_mast
This SubSeries is part of SuperSeries:
GSE48086 Genome-scale analysis in blood progenitor and mast cells reveals how lineage-affiliated transcription factors control distinct regulatory programs
BioProject PRJNA208892
SRA SRP026165

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Supplementary file Size Download File type/resource
GSE48085_RAW.tar 2.9 Gb (http)(custom) TAR (of BED, BEDGRAPH, FPKM_TRACKING)
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Raw data are available in SRA
Processed data provided as supplementary file

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