The role of RUNX2 and BHLHE40 in pathologically relevant CD4-positive tissue-resident T-cells in Crohn's disease. (CITE-seq, CD4+ T cell)
Single-cell RNA-seq · human · 18 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Samples
- 18 samples: 18 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 GSE281504_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1184155 and SRA study SRP544233. 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 18 sample titles: 18 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.
- GSM8622144 CD1, mRNA-derived cDNA
- GSM8622145 CD1, TCR-derived cDNA
- GSM8622146 CD1, HTO-derived cDNA
- GSM8622147 Ctrl1, mRNA-derived cDNA
- GSM8622148 Ctrl1, TCR-derived cDNA
- GSM8622149 Ctrl1, HTO-derived cDNA
- GSM8622150 Ctrl2, mRNA-derived cDNA
- GSM8622151 Ctrl2, TCR-derived cDNA
- GSM8622152 Ctrl2, HTO-derived cDNA
- GSM8622153 CD2, mRNA-derived cDNA
- GSM8622154 CD2, TCR-derived cDNA
- GSM8622155 CD2, HTO-derived cDNA
- GSM8622156 Ctrl3, mRNA-derived cDNA
- GSM8622157 Ctrl3, TCR-derived cDNA
- GSM8622158 Ctrl3, HTO-derived cDNA
- GSM8622159 CD3 mRNA-derived cDNA
- GSM8622160 CD3, TCR-derived cDNA
- GSM8622161 CD3, HTO-derived cDNA
- GSE280714 The role of RUNX2 and BHLHE40 in pathologically relevant CD4-positive tissue-resident T-cells in Crohn's disease. (scMultiome) 12 samples shares bhlhe40, runx2, cd4, tissue-resident, pathologically, cd4-positive, relevant
- GSE335819 Single-Cell RNA sequencing reveals clonally-expanded CD4+ tissue-resident memory T cells in Histidyl-tRNA Synthetase-induced myositis [1] 16 samples shares cd4, tissue-resident
- GSE291286 Clinical cure of chronic hepatitis B is associated with priming and perpetuation of hepatic CD4+ T cell responses 98 samples shares cd4
- GSE308745 The Cd4+ T cell population Partners with Tpex CD8 T cells to mediate Antitumor Immunity in the Tumor Microenvironment.[PB cohort2] 87 samples shares cd4
- GSE233046 Inflammation durably imprints memory CD4+ T cells 73 samples shares cd4
- GSE266862 Single-cell RNA sequencing comparison of CD4+, CD8+ and T-cell receptor γδ+ cutaneous T-cell lymphomas reveals subset-specific molecular phenotypes 44 samples shares cd4
- GSE278119 Clonally expanded effector CD4+ cytotoxic T lymphocytes are associated with severe neurological adverse events after immune checkpoint inhibitor therapy 44 samples shares cd4
- GSE277428 NKG2D-mediated cytotoxicity of CD4 cytotoxic T cells in multiple myeloma 27 samples shares cd4
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.