The role of RUNX2 and BHLHE40 in pathologically relevant CD4-positive tissue-resident T-cells in Crohn's disease. (scMultiome)
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 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
- Homo sapiens (human)
- Samples
- 12 samples: 12 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
- Multi-omics uncovers transcriptional programs of gut-resident memory CD4+ T cells in Crohn's diseaseThe Journal of experimental medicine · 2025
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 GSE280714_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 PRJNA1180087 and SRA study SRP542210. 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 12 sample titles: 12 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.
- GSM8604675 CD1_scMultiome_ATAC
- GSM8604676 CD1_scMultiome_GEX
- GSM8604677 Ctrl1_scMultiome_ATAC
- GSM8604678 Ctrl1_scMultiome_GEX
- GSM8604679 Ctrl2_scMultiome_ATAC
- GSM8604680 Ctrl2_scMultiome_GEX
- GSM8604681 CD2_scMultiome_ATAC
- GSM8604682 CD2_scMultiome_GEX
- GSM8604683 Ctrl3_scMultiome_ATAC
- GSM8604684 Ctrl3_scMultiome_GEX
- GSM8604685 CD3_scMultiome_ATAC
- GSM8604686 CD3_scMultiome_GEX
- GSE281504 The role of RUNX2 and BHLHE40 in pathologically relevant CD4-positive tissue-resident T-cells in Crohn's disease. (CITE-seq, CD4+ T cell) 18 samples shares bhlhe40, runx2, tissue-resident, pathologically, cd4-positive, relevant, t-cells
- GSE275362 The role of RUNX2 and BHLHE40 in pathologically relevant CD4-positive tissue-resident T-cells in Crohn's disease. 12 samples shares bhlhe40, runx2, tissue-resident, pathologically, cd4-positive, relevant, t-cells
- GSE303141 The role of RUNX2 and BHLHE40 in pathologically relevant CD4-positive tissue-resident T-cells in Crohn's disease. (CUT&RUN) 12 samples shares bhlhe40, runx2, tissue-resident, pathologically, cd4-positive, relevant, t-cells
- GSE301689 The role of RUNX2 and BHLHE40 in pathologically relevant CD4-positive tissue-resident T-cells in Crohn's disease. (CITE-seq, CD4+ T cell) II 9 samples shares bhlhe40, runx2, tissue-resident, pathologically, cd4-positive, relevant, t-cells
- GSE300850 The role of RUNX2 and BHLHE40 in pathologically relevant CD4-positive tissue-resident T-cells in Crohn's disease. (RNA-seq, CD4+ T cell, part2) 6 samples shares bhlhe40, runx2, tissue-resident, pathologically, cd4-positive, relevant, t-cells
- GSE300848 The role of RUNX2 and BHLHE40 in pathologically relevant CD4-positive tissue-resident T-cells in Crohn's disease. (RNA-seq, CD4+ T cell, part1) 3 samples shares bhlhe40, runx2, tissue-resident, pathologically, cd4-positive, relevant, t-cells
- GSE281509 The role of RUNX2 and BHLHE40 in pathologically relevant CD4 positive tissue-resident T-cells in Crohn's disease. (CITE-seq, CD4+ CD103+ T cell) 6 samples shares bhlhe40, runx2, tissue-resident, pathologically, relevant, t-cells
- GSE232239 CD49a expression and induction of cytotoxicity on human tissue-resident CD8+ T cells is controlled by RUNX2 and RUNX3 transcription factor activity 55 samples shares runx2, tissue-resident
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.