A cell-intrinsic glucocorticoid biosynthesis and sensing circuit maintains homeostatic Th17 cell state [ATAC-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
- 12 samples: 3 × WT_Ctrl vs 3 × WT_Dex vs 3 × KO_Ctrl vs 3 × KO_DexGroups 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 GSE320348_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 PRJNA1427637 and SRA study SRP679014. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM9541279 WT_Ctrl_1 WT_Ctrl
- GSM9541280 WT_Ctrl_2 WT_Ctrl
- GSM9541281 WT_Ctrl_3 WT_Ctrl
- GSM9541282 WT_Dex_1 WT_Dex
- GSM9541283 WT_Dex_2 WT_Dex
- GSM9541284 WT_Dex_3 WT_Dex
- GSM9541285 KO_Ctrl_1 KO_Ctrl
- GSM9541286 KO_Ctrl_2 KO_Ctrl
- GSM9541287 KO_Ctrl_3 KO_Ctrl
- GSM9541288 KO_Dex_1 KO_Dex
- GSM9541289 KO_Dex_2 KO_Dex
- GSM9541290 KO_Dex_3 KO_Dex
- GSE296502 A cell-intrinsic glucocorticoid biosynthesis and sensing circuit maintains homeostatic Th17 cell state 46 samples shares th17, cell-intrinsic, glucocorticoid, biosynthesis, homeostatic, maintains, sensing
- GSE296482 A cell-intrinsic glucocorticoid biosynthesis and sensing circuit maintains homeostatic Th17 cell state [RNA-seq] 31 samples shares th17, cell-intrinsic, glucocorticoid, biosynthesis, homeostatic, maintains, sensing
- GSE233905 Transcription factor TCF1 binds Rorgt and orchestrates a regulatory network that determines homeostatic Th17 cell state [ATAC-seq] 13 samples shares th17, homeostatic, atac-seq
- 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, atac-seq
- GSE250576 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. 10 samples shares th17, atac-seq
- GSE296401 Interleukin-23 promotes a pro-inflammatory Th17 cell state by stabilizing RORγt and suppressing glucocorticoid receptor activity II 38 samples shares th17, glucocorticoid
- GSE233908 Transcription factor TCF1 binds Rorgt and orchestrates a regulatory network that determines homeostatic Th17 cell state 21 samples shares th17, homeostatic
- GSE298162 Mecp2 acts as a key stabilizer of glucocorticoid-induced genes in active chromatin regions [scATAC-Seq] 81 samples shares glucocorticoid, atac-seq
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.