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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 May 15, 2019
Contact name Fred P. Davis
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
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 116.8 Mb (ftp)(http) BW 135.4 Mb (ftp)(http) BW
GSE96724_TbetKO.CD4.ChIP_STAT1.IFNb_3d_peaks.bed.gz 33.7 Kb (ftp)(http) BED 34.3 Mb (ftp)(http) BW
GSE96724_TbetKO.CD4.ChIP_STAT1.IFNg_3d_peaks.bed.gz 35.4 Kb (ftp)(http) BED 37.5 Mb (ftp)(http) BW
GSE96724_TbetKO.CD4.ChIP_STAT1.nc_3d_peaks.bed.gz 51.2 Kb (ftp)(http) BED 28.1 Mb (ftp)(http) BW
GSE96724_TbetKO.CD4.ChIP_STAT2.IFNb_3d_peaks.bed.gz 233.7 Kb (ftp)(http) BED 179.2 Mb (ftp)(http) BW
GSE96724_TbetKO.CD4.ChIP_STAT2.IFNg_3d_peaks.bed.gz 120.2 Kb (ftp)(http) BED 133.4 Mb (ftp)(http) BW
GSE96724_TbetKO.CD4.ChIP_STAT2.nc_3d_peaks.bed.gz 117.2 Kb (ftp)(http) BED 119.7 Mb (ftp)(http) BW 212.3 Mb (ftp)(http) BW 231.8 Mb (ftp)(http) BW 235.7 Mb (ftp)(http) BW
GSE96724_TbetKO.ChIP_K27Ac.IFNb.3d_peaks.bed.gz 500.9 Kb (ftp)(http) BED 229.0 Mb (ftp)(http) BW
GSE96724_TbetKO.ChIP_K27Ac.IFNg.3d_peaks.bed.gz 506.0 Kb (ftp)(http) BED 295.1 Mb (ftp)(http) BW 476.7 Kb (ftp)(http) BED 258.7 Mb (ftp)(http) BW
GSE96724_TbetKO.ChIP_K4m1.IFNg.3d_peaks.bed.gz 751.1 Kb (ftp)(http) BED 314.1 Mb (ftp)(http) BW 321.5 Mb (ftp)(http) BW 288.2 Mb (ftp)(http) BW 294.7 Mb (ftp)(http) BW
GSE96724_WT.ChIP_K27Ac.IFNb.3d_peaks.bed.gz 496.7 Kb (ftp)(http) BED 272.2 Mb (ftp)(http) BW
GSE96724_WT.ChIP_K27Ac.IFNg.3d_peaks.bed.gz 502.6 Kb (ftp)(http) BED 242.8 Mb (ftp)(http) BW 467.7 Kb (ftp)(http) BED 225.4 Mb (ftp)(http) BW
GSE96724_WT.ChIP_K4m1.IFNg.3d_peaks.bed.gz 730.0 Kb (ftp)(http) BED 286.5 Mb (ftp)(http) BW 279.6 Mb (ftp)(http) BW 421.2 Mb (ftp)(http) 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 31.0 Mb (ftp)(http) BW
GSE96724_wt.CD4.ChIP_STAT1.IFNg_3d_peaks.bed.gz 39.1 Kb (ftp)(http) BED 43.9 Mb (ftp)(http) BW
GSE96724_wt.CD4.ChIP_STAT1.nc_3d_peaks.bed.gz 40.6 Kb (ftp)(http) BED 25.7 Mb (ftp)(http) BW
GSE96724_wt.CD4.ChIP_STAT2.IFNb_3d_peaks.bed.gz 198.6 Kb (ftp)(http) BED 168.3 Mb (ftp)(http) BW
GSE96724_wt.CD4.ChIP_STAT2.IFNg_3d_peaks.bed.gz 87.7 Kb (ftp)(http) BED 140.4 Mb (ftp)(http) BW
GSE96724_wt.CD4.ChIP_STAT2.nc_3d_peaks.bed.gz 103.2 Kb (ftp)(http) BED 176.3 Mb (ftp)(http) BW
GSE96724_wt.CD4.ChIP_Tbet.IFNb_3d_peaks.bed.gz 61.1 Kb (ftp)(http) BED 54.4 Mb (ftp)(http) BW
GSE96724_wt.CD4.ChIP_Tbet.IFNg_3d_peaks.bed.gz 125.1 Kb (ftp)(http) BED 71.3 Mb (ftp)(http) BW
GSE96724_wt.CD4.ChIP_Tbet.nc_3d_peaks.bed.gz 57.6 Kb (ftp)(http) BED 66.8 Mb (ftp)(http) BW 239.5 Mb (ftp)(http) BW 234.7 Mb (ftp)(http) BW 223.3 Mb (ftp)(http) BW
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Raw data are available in SRA
Processed data are available on Series record

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