T cell-intrinsic cGAS-CTCF regulation maintains regulatory T cell development and function
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 30 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Mus musculus (mouse)
- Samples
- 30 samples: 8 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE301763_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1287524 and SRA study SRP598132. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 26 samples.
How we read this: 8 replicated groups read from 30 sample titles; they account for 26 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM9087060 WT CD25+Foxp3- preTreg ATAC, rep1 WT CD25+Foxp3- preTreg …
- GSM9087061 WT CD25+Foxp3- preTreg ATAC, rep2 WT CD25+Foxp3- preTreg …
- GSM9087062 WT CD25+Foxp3- preTreg ATAC, rep3 WT CD25+Foxp3- preTreg …
- GSM9087063 Cgas KO CD25+Foxp3- preTreg ATAC, rep1 Cgas KO CD25+Foxp3- pre…
- GSM9087064 Cgas KO CD25+Foxp3- preTreg ATAC, rep2 Cgas KO CD25+Foxp3- pre…
- GSM9087065 Cgas KO CD25+Foxp3- preTreg ATAC, rep3 Cgas KO CD25+Foxp3- pre…
- GSM9087066 WT tTreg ATAC, rep1 WT tTreg ATAC,
- GSM9087067 WT tTreg ATAC, rep2 WT tTreg ATAC,
- GSM9087068 WT tTreg ATAC, rep3 WT tTreg ATAC,
- GSM9087069 Cgas KO tTreg ATAC, rep1 Cgas KO tTreg ATAC,
- GSM9087070 Cgas KO tTreg ATAC, rep2 Cgas KO tTreg ATAC,
- GSM9087071 Cgas KO tTreg ATAC, rep3 Cgas KO tTreg ATAC,
- GSM9087072 WT CTCF CUT&Run, rep1 WT CTCF CUT&Run,
- GSM9087073 WT CTCF CUT&Run, rep2 WT CTCF CUT&Run,
- GSM9087074 WT CTCF CUT&Run, rep3 WT CTCF CUT&Run,
- GSM9087075 Cgas KO CTCF CUT&Run, rep1 Cgas KO CTCF CUT&Run,
- GSM9087076 Cgas KO CTCF CUT&Run, rep2 Cgas KO CTCF CUT&Run,
- GSM9087077 Cgas KO CTCF CUT&Run, rep3 Cgas KO CTCF CUT&Run,
- GSM9087078 WT tTreg in situ Hi-C, rep1 WT tTreg in situ Hi-C,
- GSM9087079 WT tTreg in situ Hi-C, rep2 WT tTreg in situ Hi-C,
- GSM9087080 WT tTreg in situ Hi-C, rep3 WT tTreg in situ Hi-C,
- GSM9087081 WT tTreg in situ Hi-C, rep4 WT tTreg in situ Hi-C,
- GSM9087082 Cgas KO tTreg in situ Hi-C, rep1 Cgas KO tTreg in situ H…
- GSM9087083 Cgas KO tTreg in situ Hi-C, rep2 Cgas KO tTreg in situ H…
- GSM9087084 Cgas KO tTreg in situ Hi-C, rep3 Cgas KO tTreg in situ H…
- GSM9087085 Cgas KO tTreg in situ Hi-C, rep4 Cgas KO tTreg in situ H…
- GSM9087086 WT CD4+CCR7+ thymocytes
- GSM9087087 Cgas KO CD4+CCR7+ thymocytes
- GSM9087088 WT CD4+CCR7+ thymocytes, TCR-seq
- GSM9087089 Cgas KO CD4+CCR7+ thymocytes, TCR-seq
- GSE301663 T cell-intrinsic cGAS-CTCF regulation maintains regulatory T cell development and function [Hi-C] 8 samples shares cell-intrinsic, regulatory, cgas-ctcf, maintains
- GSE296502 A cell-intrinsic glucocorticoid biosynthesis and sensing circuit maintains homeostatic Th17 cell state 46 samples shares cell-intrinsic, maintains
- GSE296482 A cell-intrinsic glucocorticoid biosynthesis and sensing circuit maintains homeostatic Th17 cell state [RNA-seq] 31 samples shares cell-intrinsic, maintains
- GSE292261 A dynamic gene regulatory code drives synaptic development of hippocampal granule cells [SS2] 576 samples shares regulatory
- GSE291186 Emergency Myelopoiesis in Murine Arthritis Results in Cell-Intrinsic Changes in Dendritic Cell Development and Function 26 samples shares cell-intrinsic
- GSE274992 Splenic fibroblasts control marginal zone B-cell movement and function via two distinct Notch2-dependent regulatory programs 119 samples shares regulatory
- GSE322558 Physiologic variation in sperm miRNAs tunes embryonic gene regulatory programs and developmental outcomes 622 samples shares regulatory
- GSE297451 Temporal and Context-Dependent Requirements for the Transcription Factor Foxp3 in Regulatory T Cell Development and Maintenance [RNA-seq] 70 samples shares regulatory
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.