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GEO help: Mouse over screen elements for information. |
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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
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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.
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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
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Contributor(s) |
Gounari F, Quandt J |
Citation(s) |
33664518 |
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Submission date |
Nov 05, 2019 |
Last update date |
Jul 14, 2021 |
Contact name |
Fotini Gounari |
E-mail(s) |
fgounari@uchicago.edu
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Phone |
773-834-6723
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Organization name |
University of Chicago
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Department |
Medicine
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Lab |
Fotini Gounari
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Street address |
924 E 27th Street, JFK
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City |
Chicago |
State/province |
IL |
ZIP/Postal code |
60637 |
Country |
USA |
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Platforms (1) |
GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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Samples (13)
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Relations |
BioProject |
PRJNA587731 |
SRA |
SRP228606 |
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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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