← BioTransfer GEO Dataset Finder
GEO series

High-dimensional profiling uncovers heterogeneity, lineage-specific precursors and inflammation-induced changes in the mononuclear phagocyte compartment of the human intestine

GSE309239 Homo sapiens (human) Single-cell RNA-seq 28 samples Submitted 2025/12/18 Platform GPL16791Platform GPL18573Platform GPL24676
At a glance

Single-cell RNA-seq · human · 28 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
28 samples: 28 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
Heterogeneity of the intestinal mononuclear phagocyte compartment in health and inflammatory bowel diseaseScience immunology · 2025
Summary (written by the submitters)
With use of single-cell omics this study explore mononuclear phagocyte complexity of the human intestinal lamina propria in health and IBD. The study identifies distinct dendritic cell and macrophage subsets, lineage specific precursors and state specific signatures.
Published in
Heterogeneity of the intestinal mononuclear phagocyte compartment in health and inflammatory bowel disease
Fenton TM, Wulff L, Väänänen V et al. · Science immunology 2025 · PMID 41385609 · doi:10.1126/sciimmunol.adz8650
This dataset
Open GSE309239 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 GSE309239_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 PRJNA1334397. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41385609) ↗
Study design
28 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 28 sample titles: 28 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.

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.