Transcription factor TCF1 binds Rorgt and orchestrates a regulatory network that determines homeostatic Th17 cell state
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 21 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
- 21 samples: 21 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.
- Paper
- Transcription factor TCF1 binds to RORγt and orchestrates a regulatory network that determines homeostatic Th17 cell stateImmunity · 2024
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 GSE233908_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 PRJNA978551 and SRA study SRP440688. 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 21 sample titles: 21 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.
- GSM7438922 WT_1_dLN
- GSM7438923 WT_2_dLN
- GSM7438924 WT_3_dLN
- GSM7438925 WT_5_dLN
- GSM7438926 WT_6_dLN
- GSM7438927 WT_7_dLN
- GSM7438928 KO_1_dLN
- GSM7438929 KO_2_dLN
- GSM7438930 KO_3_dLN
- GSM7438931 KO_4_dLN
- GSM7438932 KO_5_dLN
- GSM7438933 KO_6_dLN
- GSM7438934 KO_7_dLN
- GSM7438949 KO_1_dLN RNA
- GSM7438950 KO_2_dLN RNA
- GSM7438951 KO_3_dLN RNA
- GSM7438952 KO_4_dLN RNA
- GSM7438953 WT_1_dLN RNA
- GSM7438954 WT_2_dLN RNA
- GSM7438955 WT_3_dLN RNA
- GSM7438956 WT_4_dLN RNA
- GSE267584 Enhancer-driven gene regulatory networks reveal transcription factors governing T cell adaptation and differentiation in the tumor microenvironment. 22 samples shares transcription, regulatory, network
- GSE306744 Pre-division TCF1 downregulation determines long-term effector and memory CD8 T cell fates [RNA-Seq] 31 samples shares tcf1, determines
- GSE305064 FOXP3 Expression Depends on Cell-Type Specific Cis-Regulatory Element and Transcription Factor Circuitry [mouse_Tconv_ChIP-seq] 15 samples shares transcription, regulatory
- GSE234974 Pan-cancer mapping of single CD8+ T cell profiles reveals a TCF1:CXCR6 axis regulating CD28 co-stimulation and anti-tumor immunity I 24 samples shares tcf1
- GSE318707 ST8Sia6-dependent glycosylation restrains gut inflammation and pathogenic Th1 and Th17 programs 18 samples shares th17
- GSE290258 Satb1 directs the differentiation of TH17 cells through suppression of IL-2 expression [scMultiom ATAC/RNA-seq] 12 samples shares th17
- GSE252358 Acetylcyssteine synergizes PD-1 blockers against colorectal cancer progression by promoting TCF1+PD1+CD8+ T cell differentiation in mice 10 samples shares tcf1
- GSE248586 A conserved epithelial wound-like transcriptional program driven by FOSL1 underlies malignant progression of pancreatic ductal adenocarcinoma 57 samples shares transcription
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.