ATAC-seq of Satb1 conditional KO in CD4+ naïve T cells reveals epigenetic role of Satb1 in developing Th17 T cells by controlling the accessibility of Il2, thereby inhibiting IL-2 signaling in the initial stages of T cell differentiation.
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 10 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
- 10 samples: 10 samples, each with a distinct title — no replicated groupsGroups 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.
Read the full summary ↓
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 GSE250576_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 PRJNA1054565 and SRA study SRP479033. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 10 sample titles: 10 distinct titles with little repetition. 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.
- GSM7981900 Sample_2268_KO
- GSM7981901 Sample_2269_KO
- GSM7981902 Sample_2270_KO
- GSM7981903 Sample_2271_KO
- GSM7981904 Sample_2272_KO
- GSM7981905 Sample_2273_WT
- GSM7981906 Sample_2274_WT
- GSM7981907 Sample_2275_WT
- GSM7981908 Sample_2276_WT
- GSM7981909 Sample_2277_WT
- GSE290258 Satb1 directs the differentiation of TH17 cells through suppression of IL-2 expression [scMultiom ATAC/RNA-seq] 12 samples shares satb1, th17, il-2
- GSE296200 A20’s Linear Ubiquitin Binding Motif Restrains Pathogenic Activation of TH17/22 cells and IL-22 Driven Enteritis [ATAC-seq] 11 samples shares th17, il-2
- GSE197425 TGF-β specifies TFH versus TH17 cell fates in murine CD4+ T cells through c-Maf (Seq03, bulk-RNAseq) 34 samples shares th17, cd4
- GSE222456 Distinctive CD39+CD9+ lung interstitial macrophages suppress IL-23/Th17-mediated neutrophilic asthma by inhibiting NETosis [scRNA-Seq] 12 samples shares th17, il-2
- GSE325227 CD69 regulates the tissue dynamics of epigenetically imprinted memory CD4+ T cells [RNA-seq_ATAC-seq] 22 samples shares cd4, epigenetic
- GSE243710 Analysis of three-dimensional enhancer network regulated by CTCF in CD4+ T cells [ChIP-seq] 33 samples shares cd4
- GSE302620 Oncolytic virus therapy mobilizes tumor-resident CD4+ bystander T cells to restore systemic anti-microbial immunity [ATAC-seq] 16 samples shares cd4
- GSE314532 Cis-regulation of IL-22 gene in type 3 immune cells 16 samples shares il-2
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.