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Series GSE148672 Query DataSets for GSE148672
Status Public on Jun 29, 2020
Title Genome-wide maps of chromatin state of IRF5+/+ and IRF5-/- CD4+ mouse T cells
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Genetic variants in IRF5 are associated with multiple immune-mediated diseases. IRF5 has been predominantly focused on for its regulation of myeloid-derived cells. We found that IRF5 contributes to CD4+ T cell outcomes and that it regulates early T cell receptor-initiated signaling and subsequently translocates to the nucleus where it binds to promoters of various genes regulated with T cell activation. We report the chromatin state of freshly isolated and activated IRF5+/+ and IRF5-/- CD4+ T cells in vitro. While there are minimal differential peaks between freshly isolated IRF5+/+ and IRF5-/- CD4+ T cells, once activated multiple differential peaks are observed between IRF5+/+ and IRF5-/- CD4+ T cells.
 
Overall design ATAC-seq in untreated and 72 hour activated IRF5+/+ and IRF5-/- mouse CD4+ T cells in vitro
 
Contributor(s) Abraham C, Yan J, Zhao D
Citation(s) 32610123
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 AI120369 Mechanisms Regulating Innate Immune Responses YALE UNIVERSITY CLARA ABRAHAM
R01 DK099097 Functional outcomes of inflammatory bowel disease associated variants YALE UNIVERSITY CLARA ABRAHAM
Submission date Apr 14, 2020
Last update date Sep 28, 2020
Contact name Clara Abraham
Organization name Yale University
Street address 333 Cedar Street, 1080 LMP
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (15)
GSM4476470 CD4+ T cells, KO-0h-1
GSM4476471 CD4+ T cells, KO-0h-3
GSM4476472 CD4+ T cells, KO-0h-4
Relations
BioProject PRJNA625322
SRA SRP256377

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
GSE148672_KO0h_0_peaks.txt.gz 1.5 Mb (ftp)(http) TXT
GSE148672_KO0h_0_treat_pileup.bw 531.6 Mb (ftp)(http) BW
GSE148672_KO0h_finalPeaks.txt.gz 1.0 Mb (ftp)(http) TXT
GSE148672_KO72h_0_peaks.txt.gz 2.4 Mb (ftp)(http) TXT
GSE148672_KO72h_0_treat_pileup.bw 677.2 Mb (ftp)(http) BW
GSE148672_KO72h_finalPeaks.txt.gz 1.3 Mb (ftp)(http) TXT
GSE148672_RAW.tar 3.0 Gb (http)(custom) TAR (of BW, TXT)
GSE148672_WT0h_0_peaks.txt.gz 1.8 Mb (ftp)(http) TXT
GSE148672_WT0h_0_treat_pileup.bw 605.4 Mb (ftp)(http) BW
GSE148672_WT0h_finalPeaks.txt.gz 1.1 Mb (ftp)(http) TXT
GSE148672_WT72h_0_peaks.txt.gz 2.6 Mb (ftp)(http) TXT
GSE148672_WT72h_0_treat_pileup.bw 714.5 Mb (ftp)(http) BW
GSE148672_WT72h_finalPeaks.txt.gz 1.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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