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Series GSE40918 Query DataSets for GSE40918
Status Public on Sep 20, 2012
Title A validated regulatory network for Th17 cell specification
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Th17 cells have critical roles in mucosal defense and are major contributors to inflammatory disease. Their differentiation requires the nuclear hormone receptor RORγt working with multiple other essential transcription factors (TFs). We have used an iterative systems approach, combining genome-wide TF occupancy, expression profiling of TF mutants, and expression time series to delineate the Th17 global transcriptional regulatory network. We find that cooperatively-bound BATF and IRF4 contribute to initial chromatin accessibility, and with STAT3 initiate a transcriptional program that is then globally tuned by the lineage-specifying TF RORγt, which plays a focal deterministic role at key loci. Integration of multiple datasets allowed inference of an accurate predictive model that we computationally and experimentally validated, identifying multiple new Th17 regulators, including Fosl2, a key determinant of cellular plasticity. This interconnected network can be used to investigate new therapeutic approaches to manipulate Th17 functions in the setting of inflammatory disease.
Overall design 143 RNA-seq, 83 ChIP-seq, 65 ChIP-seq controls, and 16 FAIRE-seq
Contributor(s) Ciofani M, Madar A, Galan C, Sellars M, Mace K, Pauli F, Agarwal A, Huang W, Parkurst CN, Muratet M, Newberry KM, Meadows S, Greenfield A, Yang Y, Jain P, Kirigin FK, Birchmerier C, Wagner EF, Murphy KM, Myers RM, Bonneau R, Littman DR
Citation(s) 23021777
Submission date Sep 17, 2012
Last update date May 15, 2019
Contact name Ashish Agarwal
Organization name Solvuu
Street address 150 E 44th St #27E
City New York
State/province NY
ZIP/Postal code 10017
Country USA
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (307)
GSM1004784 SL3039
GSM1004785 SL3192
GSM1004786 SL3033
BioProject PRJNA175364
SRA SRP015773

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
GSE40918_Inferelator_Immgen.txt.gz 1.2 Mb (ftp)(http) TXT
GSE40918_Inferelator_RNAseq.txt.gz 1.3 Mb (ftp)(http) TXT
GSE40918_RAW.tar 132.9 Mb (http)(custom) TAR (of TXT)
GSE40918_README_supplementary_files.txt 4.0 Kb (ftp)(http) TXT
GSE40918_Th17.batf.wt.vs.Th17.batf.ko_Aug_2_2012.txt.gz 848.2 Kb (ftp)(http) TXT
GSE40918_Th17.fosl2.wt.vs.Th17.fosl2.ko_Aug_2_2012.txt.gz 841.5 Kb (ftp)(http) TXT
GSE40918_Th17.hif1a.wt.vs.Th17.hif1a.ko_Aug_2_2012.txt.gz 1.1 Mb (ftp)(http) TXT
GSE40918_Th17.ikzf3.wt.vs.Th17.ikzf3.ko_Aug_2_2012.txt.gz 784.8 Kb (ftp)(http) TXT
GSE40918_Th17.irf4.wt.vs.Th17.irf4.ko_Aug_2_2012.txt.gz 1.1 Mb (ftp)(http) TXT
GSE40918_Th17.maf.wt.vs.Th17.maf.ko_Aug_2_2012.txt.gz 1.1 Mb (ftp)(http) TXT
GSE40918_Th17.rorc.wt.vs.Th17.rorc.ko_Aug_2_2012.txt.gz 822.1 Kb (ftp)(http) TXT
GSE40918_Th17.siNonTar.24hRPMI.vs.Th17.siEtv6.24hRPMI_Aug_2_2012.txt.gz 1.2 Mb (ftp)(http) TXT
GSE40918_Th17.siNonTar.24hScreen.vs.Th17.siAes.24hScreen_Aug_2_2012.txt.gz 816.7 Kb (ftp)(http) TXT
GSE40918_Th17.siNonTar.24hScreen.vs.Th17.siAtf6.24hScreen_Aug_2_2012.txt.gz 1.1 Mb (ftp)(http) TXT
GSE40918_Th17.siNonTar.24hScreen.vs.Th17.siBcl11b.24hScreen_Aug_2_2012.txt.gz 1.1 Mb (ftp)(http) TXT
GSE40918_Th17.siNonTar.24hScreen.vs.Th17.siCcr6.24hScreen_Aug_2_2012.txt.gz 1.1 Mb (ftp)(http) TXT
GSE40918_Th17.siNonTar.24hScreen.vs.Th17.siCrem.24hScreen_Aug_2_2012.txt.gz 1.1 Mb (ftp)(http) TXT
GSE40918_Th17.siNonTar.24hScreen.vs.Th17.siDdit3.24hScreen_Aug_2_2012.txt.gz 1.1 Mb (ftp)(http) TXT
GSE40918_Th17.siNonTar.24hScreen.vs.Th17.siEgr2.24hScreen_Aug_2_2012.txt.gz 1.1 Mb (ftp)(http) TXT
GSE40918_Th17.siNonTar.24hScreen.vs.Th17.siId2.24hScreen_Aug_2_2012.txt.gz 1.0 Mb (ftp)(http) TXT
GSE40918_Th17.siNonTar.24hScreen.vs.Th17.siInhba.24hScreen_Aug_2_2012.txt.gz 1.2 Mb (ftp)(http) TXT
GSE40918_Th17.siNonTar.24hScreen.vs.Th17.siJmjd6.24hScreen_Aug_2_2012.txt.gz 1.1 Mb (ftp)(http) TXT
GSE40918_Th17.siNonTar.24hScreen.vs.Th17.siKdm6b.24hScreen_Aug_2_2012.txt.gz 1.1 Mb (ftp)(http) TXT
GSE40918_Th17.siNonTar.24hScreen.vs.Th17.siLef1.24hScreen_Aug_2_2012.txt.gz 1.1 Mb (ftp)(http) TXT
GSE40918_Th17.siNonTar.24hScreen.vs.Th17.siNfatc2.24hScreen_Aug_2_2012.txt.gz 1.1 Mb (ftp)(http) TXT
GSE40918_Th17.siNonTar.24hScreen.vs.Th17.siPrkrir.24hScreen_Aug_2_2012.txt.gz 1.1 Mb (ftp)(http) TXT
GSE40918_Th17.siNonTar.24hScreen.vs.Th17.siRorc.24hScreen_Aug_2_2012.txt.gz 1.1 Mb (ftp)(http) TXT
GSE40918_Th17.siNonTar.24hScreen.vs.Th17.siSatb1.24hScreen_Aug_2_2012.txt.gz 1.1 Mb (ftp)(http) TXT
GSE40918_Th17.siNonTar.24hScreen.vs.Th17.siSirt2.24hScreen_Aug_2_2012.txt.gz 1.1 Mb (ftp)(http) TXT
GSE40918_Th17.siNonTar.24hScreen.vs.Th17.siSki.24hScreen_Aug_2_2012.txt.gz 1.1 Mb (ftp)(http) TXT
GSE40918_Th17.siNonTar.24hScreen.vs.Th17.siTrib3.24hScreen_Aug_2_2012.txt.gz 1.0 Mb (ftp)(http) TXT
GSE40918_Th17.siNonTar.24hScreen.vs.Th17.siZfp36l2.24hScreen_Aug_2_2012.txt.gz 1.1 Mb (ftp)(http) TXT
GSE40918_Th17.stat3.wt.vs.Th17.stat3.ko_Aug_2_2012.txt.gz 1.1 Mb (ftp)(http) TXT
GSE40918_pCRMs_5TFs_th17.txt.gz 3.7 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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