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Series GSE40727 Query DataSets for GSE40727
Status Public on Sep 13, 2012
Title ChIPseq analysis of IRF4 and BATF in immune cells
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Purpose: The purpose of this study is to find the binding partner of IRF4 in the context of Th17- cell differentiation. To this end, we have used ChIPseq analysis followed by de novo motif search around genome-wide binding sites to identify BATF as the binding partner for IRF4 in the context of not only Th17 cells but other immune cell types as well.
Overall design Naïve T-cells isolated from the spleen of C57BL/6J mice are cultured under Th17, Th2 or Th0 polarizing conditions for 42 hrs and subject to ChIP using IRF4 and/or BATF antibodies followed by high-throughput sequencing. Bone marrow derived dendritic cells (BMDCs) were stimulated with LPS for 6hrs and similrly subjected to ChIPseq analysis with IRF4.
Contributor(s) Agrawal S, Zeng W, Lugt B
Citation(s) 22983707
Submission date Sep 10, 2012
Last update date May 15, 2019
Contact name Smita Agrawal
Organization name Genentech Inc.
Department Immunology
Street address 1 DNA Way
City South San Francisco
State/province CA
ZIP/Postal code 94080
Country USA
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (9)
GSM999800 Th17 42hr IRF4
GSM999801 Th17 42hr BATF
GSM999802 Th2 42hr IRF4
This SubSeries is part of SuperSeries:
GSE40483 A genomic regulatory element that directs assembly and function of immunespecific AP-1-IRF complexes
BioProject PRJNA174767
SRA SRP015676

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
GSE40727_RAW.tar 59.6 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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