NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE139960 Query DataSets for GSE139960
Status Public on Oct 01, 2020
Title Wnt/β-catenin activation epigenetically reprograms Regulatory T cells in IBD and progression to dysplasia
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Previous work indicated that β-catenin/TCF-1 occupy DNA together with Foxp3. Thus, we anticipated that precise mapping of TCF-1 and Foxp3 co-binding in Tregs, could provide a molecular explanation for our phenotypic observations. To address this, we analyzed TCF-1 DNA binding in Tregs through chromatin immunoprecipitation and deep sequencing (ChIPseq) in Foxp3YFP-Cre WT Tregs. Furthermore, we assessed regions of accessible chromatin in Tregs via transposase-accessible chromatin approach and deep sequencing (ATAC-seq). We also performed RNA-seq expression profiling to investigate how the changes in chromatin accessibility impacted transcription in β-catenin high Tregs.
 
Overall design mRNA profiles and ATACseq derived from of 21-day old Foxp3Cre-YFP (WT) and Foxp3Cre-YFP Ctnnb1flex3 (CAT) male mice were generated by deep sequencing, in triplicate, using Illumina
 
Contributor(s) Gounari F, Quandt J
Citation(s) 33664518
Submission date Nov 05, 2019
Last update date Jul 14, 2021
Contact name Fotini Gounari
E-mail(s) fgounari@uchicago.edu
Phone 773-834-6723
Organization name University of Chicago
Department Medicine
Lab Fotini Gounari
Street address 924 E 27th Street, JFK
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platforms (1)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (13)
GSM4150513 Tregs_WT_TCF1_ChIPseq
GSM4150514 Tregs_WT_Input_DNA
GSM4150515 Tregs_ATACseq_WT1
Relations
BioProject PRJNA587731
SRA SRP228606

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
GSE139960_RAW.tar 1.1 Gb (http)(custom) TAR (of BEDGRAPH, TXT)
GSE139960_RNAseq_CuffDiff_DiffGeneExpTest.xlsx 1.9 Mb (ftp)(http) XLSX
GSE139960_RNAseq_CuffDiff_FPKMtracking.xlsx 6.8 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.