← BioTransfer GEO Dataset Finder
GEO series

Differential effects of tofacitinib on macrophage activation contribute to lack of response in ulcerative colitis patients

GSE253006 Homo sapiens (human) Single-cell RNA-seq 23 samples Submitted 2025/05/19 Platform GPL18573
At a glance

Single-cell RNA-seq · human · 23 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
23 samples: 9 conditions, mostly in duplicateGroups 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
Differential effects of tofacitinib on macrophage activation contribute to lack of response in ulcerative colitis patientsJournal of Crohn's & colitis · 2025
Summary (written by the submitters)
The variability and unpredictability of drug efficacy in ulcerative colitis (UC) patients, including tofacitinib, an oral JAK1 and JAK3 inhibitor, remains a perplexing reality. Here, we use single-cell RNA sequencing (scRNA-seq) analysis of intestinal cells from UC patients receiving tofacitinib to identify the cellular subsets and genes involved in the response and/or resistance to tofacitinib.
Published in
Differential effects of tofacitinib on macrophage activation contribute to lack of response in ulcerative colitis patients
Melón-Ardanaz E, Veny M, Corraliza AM et al. · Journal of Crohn's & colitis 2025 · PMID 40320713 · doi:10.1093/ecco-jcc/jjaf076
This dataset
Open GSE253006 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE253006_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1063636 and SRA study SRP483506. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40320713) ↗
Study design
9 conditions, mostly in duplicate
TOF-005-W ×3 TOF-012-W ×3 TOF-019-W ×3 TOF-009-W ×2 TOF-011-W ×2 TOF-013-W ×2 TOF-015-W ×2 TOF-016-W ×2 +3 more

Supports a between-group comparison across 21 samples.

How we read this: 9 replicated groups read from 23 sample titles; they account for 21 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.

Samples in this study
Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

Share this dataset

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.