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Deep profiling of multiple mouse tumor microenvironments using scRNAseq

GSE310560 Mus musculus (mouse) Single-cell RNA-seq 56 samples Submitted 2026/03/05 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 56 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Mus musculus (mouse)
Samples
56 samples: 26 × HTO associated to XCRS1-POOL-SCG vs 2 × Enriched lymphoid cells from MMT-PyMT GEMM females tumors vs 2 × Enriched myeloid cells from MMT-PyMT GEMM females tumorsGroups 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 assembly of mouse and human tumor microenvironmentsNature immunology · 2026
Summary (written by the submitters)
The HuMu dataset (https://www.biorxiv.org/content/10.1101/2025.07.01.661217v1) contains single-cell sequencing data from 9 mouse tumor models that we use to dissect gene expression profiles across populations and tumor models. The data can be readily queried here https://quipi.org/app/quipi_humu
Published in
Differential assembly of mouse and human tumor microenvironments
Courau T, Jaszczak RG, Samad B et al. · Nature immunology 2026 · PMID 42156893 · doi:10.1038/s41590-026-02505-7
This dataset
Open GSE310560 in finder → Find more mouse 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 GSE310560_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 PRJNA1366508 and SRA study SRP647013. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42156893) ↗
Study design
26 × HTO associated to XCRS1-POOL-SCG vs 2 × Enriched lymphoid cells from MMT-PyMT GEMM females tumors vs 2 × Enriched myeloid cells from MMT-PyMT GEMM females tumors

Supports a between-group comparison across 30 samples.

How we read this: 3 replicated groups read from 56 sample titles; they account for 30 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

+ 16 more — browse all 56 samples with per-sample file links →

Datasets on a similar topic

Search all mouse 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.