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Series GSE36099 Query DataSets for GSE36099
Status Public on Sep 11, 2012
Title A high throughput in vivo protein-DNA mapping approach reveals principles of dynamic gene regulation in mammals (ChIP-Seq)
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Dynamic binding of transcription factors to DNA elements specifies gene expression and cell fate, in both normal physiology and disease. To date, our understanding of mammalian gene regulation has been hampered by the difficulty of directly measuring in vivo binding of large numbers of transcription factors to DNA. Here, we develop a high-throughput indexed Chromatin ImmunoPrecipitation (iChIP) method coupled to massively parallel sequencing to systematically map protein-DNA interactions. We apply iChIP to reconstruct the physical regulatory landscape of a mammalian cell, by building genome-wide binding maps for 29 transcription factors (TFs) and chromatin marks at four time points following stimulation of primary dendritic cells (DCs) with pathogen components. Using over 180,000 TF-DNA interactions in these maps, we derive an initial dynamic physical model of a mammalian cell regulatory network. Our data demonstrates that transcription factors vary substantially in their binding dynamics, genomic localization, number of binding events, and degree of interaction with other factors. Further, many of the TF-DNA interactions at stimulus-activated genes are established during differentiation and maintained in a poised state. Functionally, the TFs are organized in a hierarchy of different types: Cell differentiation factors bind most of the genes and remain largely unchanged during the stimulation. A second set of TFs bind already in the un-stimulated and preferentially target induced genes. A third set consists of TF that bind mainly after the stimuli and target specific gene functions. Together these factors determine the magnitude and timing of stimulus induced gene expression. Our method, which allowed us to map routinely temporal binding profiles of dozens of TFs, provides a foundation for future understanding of the mammalian regulatory code.
Overall design A study of dynamic binding of transcription factors in an immune cell following pathogen stimulation
Contributor(s) Garber M, Yosef N, Raychowdhury R, Thielke A, Bernstein B, Nusbaum C, Hacohen N, Regev A, Amit I
Citation(s) 22940246
Submission date Feb 27, 2012
Last update date May 15, 2019
Contact name Manuel Garber
Organization name University of Massachusetts Medical School
Department Bioinformatics and Integrative Biology
Lab Garber
Street address 55 Lake Ave North Worcester
City Worcester
State/province Massachusetts
ZIP/Postal code 01655
Country USA
Platforms (1)
GPL15103 Illumina HiSeq 1000 (Mus musculus)
Samples (117)
GSM881048 ChIP-Seq of Ahr 0 min post LPS stimulation
GSM881049 ChIP-Seq of Ahr 120 min post LPS stimulation
GSM881050 ChIP-Seq of Ahr 30 min post LPS stimulation
This SubSeries is part of SuperSeries:
GSE36104 A high throughput in vivo protein-DNA mapping approach reveals principles of dynamic gene regulation in mammals
SRA SRP011071
BioProject PRJNA155801

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
GSE36099_RAW.tar 135.5 Gb (http)(custom) TAR (of BW, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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