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Series GSE96724 Query DataSets for GSE96724
Status Public on Jun 12, 2017
Title The Transcription Factor T-bet Limits Amplification of Type I IFN Transcriptome and Circuitry in T Helper 1 Cells
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Host defense requires the specification of CD4+ helper T (Th) cells into distinct fates including Th1 cells that preferentially produce interferon γ(IFN-γ ).IFN-γ , a member of a large family of anti-pathogenic and anti-tumor IFNs, induces T-bet, a lineage defining transcription factor for Th1 cells, which in turn supports IFN-γ production in a feed-forward manner. Herein, we show a cell intrinsic role of T- bet to influence how T cells perceive their secreted product in the environment. In the absence of T-bet, IFN-γ aberrantly induces a type I IFN transcriptomic program. T-bet preferentially represses genes and pathways ordinarily activated by type I IFNs to ensure that its transcriptional response does not evoke an aberrant amplification of type I IFN signaling circuitry otherwise triggered by its own product.
 
Overall design Integrated analysis of epigenome and transcriptome data from activated T helper cells cultured under either IFN-γ or IFN-β stimulation
 
Contributor(s) Iwata S, Mikami Y, Sun HW, Brooks SR, Jankovic D, Hirahara K, Onodera A, Shih HY, Kawabe T, Jiang K, Nakayama T, Sher A, O'Shea JJ, Davis FP, Kanno Y
Citation(s) 28623086
Submission date Mar 16, 2017
Last update date Mar 21, 2019
Contact name Fred P. Davis
E-mail Fred.davis@nih.gov
Organization name NIH
Department NIAMS
Street address 9000 Rockville Pike
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (110)
GSM2538927 TbetKO.CD4.ChIP_input.IFNb_3d
GSM2538928 TbetKO.CD4.ChIP_input.IFNg_3d
GSM2538929 TbetKO.CD4.ChIP_input.nc_3d
Relations
BioProject PRJNA379464
SRA SRP102029

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
GSE96724_CD4.TbetKO.IFNg.72hr.si158.star_scaled10M_nonRRNA.bw 116.8 Mb (ftp)(http) BW
GSE96724_CD4.WT.IFNg.72hr.si252.star_scaled10M_nonRRNA.bw 135.4 Mb (ftp)(http) BW
GSE96724_TbetKO.CD4.ChIP_STAT1.IFNb_3d_peaks.bed.gz 33.7 Kb (ftp)(http) BED
GSE96724_TbetKO.CD4.ChIP_STAT1.IFNb_3d_scaled10M.bw 34.3 Mb (ftp)(http) BW
GSE96724_TbetKO.CD4.ChIP_STAT1.IFNg_3d_peaks.bed.gz 35.4 Kb (ftp)(http) BED
GSE96724_TbetKO.CD4.ChIP_STAT1.IFNg_3d_scaled10M.bw 37.5 Mb (ftp)(http) BW
GSE96724_TbetKO.CD4.ChIP_STAT1.nc_3d_peaks.bed.gz 51.2 Kb (ftp)(http) BED
GSE96724_TbetKO.CD4.ChIP_STAT1.nc_3d_scaled10M.bw 28.1 Mb (ftp)(http) BW
GSE96724_TbetKO.CD4.ChIP_STAT2.IFNb_3d_peaks.bed.gz 233.7 Kb (ftp)(http) BED
GSE96724_TbetKO.CD4.ChIP_STAT2.IFNb_3d_scaled10M.bw 179.2 Mb (ftp)(http) BW
GSE96724_TbetKO.CD4.ChIP_STAT2.IFNg_3d_peaks.bed.gz 120.2 Kb (ftp)(http) BED
GSE96724_TbetKO.CD4.ChIP_STAT2.IFNg_3d_scaled10M.bw 133.4 Mb (ftp)(http) BW
GSE96724_TbetKO.CD4.ChIP_STAT2.nc_3d_peaks.bed.gz 117.2 Kb (ftp)(http) BED
GSE96724_TbetKO.CD4.ChIP_STAT2.nc_3d_scaled10M.bw 119.7 Mb (ftp)(http) BW
GSE96724_TbetKO.CD4.ChIP_input.IFNb_3d_scaled10M.bw 212.3 Mb (ftp)(http) BW
GSE96724_TbetKO.CD4.ChIP_input.IFNg_3d_scaled10M.bw 231.8 Mb (ftp)(http) BW
GSE96724_TbetKO.CD4.ChIP_input.nc_3d_scaled10M.bw 235.7 Mb (ftp)(http) BW
GSE96724_TbetKO.ChIP_K27Ac.IFNb.3d_peaks.bed.gz 500.9 Kb (ftp)(http) BED
GSE96724_TbetKO.ChIP_K27Ac.IFNb.3d_scaled10M.bw 229.0 Mb (ftp)(http) BW
GSE96724_TbetKO.ChIP_K27Ac.IFNg.3d_peaks.bed.gz 506.0 Kb (ftp)(http) BED
GSE96724_TbetKO.ChIP_K27Ac.IFNg.3d_scaled10M.bw 295.1 Mb (ftp)(http) BW
GSE96724_TbetKO.ChIP_K27Ac.nc.3d_peaks.bed.gz 476.7 Kb (ftp)(http) BED
GSE96724_TbetKO.ChIP_K27Ac.nc.3d_scaled10M.bw 258.7 Mb (ftp)(http) BW
GSE96724_TbetKO.ChIP_K4m1.IFNg.3d_peaks.bed.gz 751.1 Kb (ftp)(http) BED
GSE96724_TbetKO.ChIP_K4m1.IFNg.3d_scaled10M.bw 314.1 Mb (ftp)(http) BW
GSE96724_TbetKO.ChIP_input.IFNb.3d_scaled10M.bw 321.5 Mb (ftp)(http) BW
GSE96724_TbetKO.ChIP_input.IFNg.3d_scaled10M.bw 288.2 Mb (ftp)(http) BW
GSE96724_TbetKO.ChIP_input.nc.3d_scaled10M.bw 294.7 Mb (ftp)(http) BW
GSE96724_WT.ChIP_K27Ac.IFNb.3d_peaks.bed.gz 496.7 Kb (ftp)(http) BED
GSE96724_WT.ChIP_K27Ac.IFNb.3d_scaled10M.bw 272.2 Mb (ftp)(http) BW
GSE96724_WT.ChIP_K27Ac.IFNg.3d_peaks.bed.gz 502.6 Kb (ftp)(http) BED
GSE96724_WT.ChIP_K27Ac.IFNg.3d_scaled10M.bw 242.8 Mb (ftp)(http) BW
GSE96724_WT.ChIP_K27Ac.nc.3d_peaks.bed.gz 467.7 Kb (ftp)(http) BED
GSE96724_WT.ChIP_K27Ac.nc.3d_scaled10M.bw 225.4 Mb (ftp)(http) BW
GSE96724_WT.ChIP_K4m1.IFNg.3d_peaks.bed.gz 730.0 Kb (ftp)(http) BED
GSE96724_WT.ChIP_K4m1.IFNg.3d_scaled10M.bw 286.5 Mb (ftp)(http) BW
GSE96724_WT.ChIP_input.IFNb.3d_scaled10M.bw 279.6 Mb (ftp)(http) BW
GSE96724_WT.ChIP_input.IFNg.3d_scaled10M.bw 421.2 Mb (ftp)(http) BW
GSE96724_WT.ChIP_input.nc.3d_scaled10M.bw 481.1 Mb (ftp)(http) BW
GSE96724_gene_expression_table.txt.gz 3.1 Mb (ftp)(http) TXT
GSE96724_wt.CD4.ChIP_STAT1.IFNb_3d_peaks.bed.gz 63.2 Kb (ftp)(http) BED
GSE96724_wt.CD4.ChIP_STAT1.IFNb_3d_scaled10M.bw 31.0 Mb (ftp)(http) BW
GSE96724_wt.CD4.ChIP_STAT1.IFNg_3d_peaks.bed.gz 39.1 Kb (ftp)(http) BED
GSE96724_wt.CD4.ChIP_STAT1.IFNg_3d_scaled10M.bw 43.9 Mb (ftp)(http) BW
GSE96724_wt.CD4.ChIP_STAT1.nc_3d_peaks.bed.gz 40.6 Kb (ftp)(http) BED
GSE96724_wt.CD4.ChIP_STAT1.nc_3d_scaled10M.bw 25.7 Mb (ftp)(http) BW
GSE96724_wt.CD4.ChIP_STAT2.IFNb_3d_peaks.bed.gz 198.6 Kb (ftp)(http) BED
GSE96724_wt.CD4.ChIP_STAT2.IFNb_3d_scaled10M.bw 168.3 Mb (ftp)(http) BW
GSE96724_wt.CD4.ChIP_STAT2.IFNg_3d_peaks.bed.gz 87.7 Kb (ftp)(http) BED
GSE96724_wt.CD4.ChIP_STAT2.IFNg_3d_scaled10M.bw 140.4 Mb (ftp)(http) BW
GSE96724_wt.CD4.ChIP_STAT2.nc_3d_peaks.bed.gz 103.2 Kb (ftp)(http) BED
GSE96724_wt.CD4.ChIP_STAT2.nc_3d_scaled10M.bw 176.3 Mb (ftp)(http) BW
GSE96724_wt.CD4.ChIP_Tbet.IFNb_3d_peaks.bed.gz 61.1 Kb (ftp)(http) BED
GSE96724_wt.CD4.ChIP_Tbet.IFNb_3d_scaled10M.bw 54.4 Mb (ftp)(http) BW
GSE96724_wt.CD4.ChIP_Tbet.IFNg_3d_peaks.bed.gz 125.1 Kb (ftp)(http) BED
GSE96724_wt.CD4.ChIP_Tbet.IFNg_3d_scaled10M.bw 71.3 Mb (ftp)(http) BW
GSE96724_wt.CD4.ChIP_Tbet.nc_3d_peaks.bed.gz 57.6 Kb (ftp)(http) BED
GSE96724_wt.CD4.ChIP_Tbet.nc_3d_scaled10M.bw 66.8 Mb (ftp)(http) BW
GSE96724_wt.CD4.ChIP_input.IFNb_3d_scaled10M.bw 239.5 Mb (ftp)(http) BW
GSE96724_wt.CD4.ChIP_input.IFNg_3d_scaled10M.bw 234.7 Mb (ftp)(http) BW
GSE96724_wt.CD4.ChIP_input.nc_3d_scaled10M.bw 223.3 Mb (ftp)(http) BW
Raw data are available in SRA
Processed data is available on Series record

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