GEO series

Single-cell RNA sequencing of intratumoral CD45+ Immune cells in a murine cancer model under chronic unpredictable mild stress (CUMS)

GSE327985 Mus musculus (mouse) Single-cell RNA-seq 12 samples Submitted 2026/05/11 Platform GPL34290

At a glance

Single-cell RNA-seq · mouse · 12 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: 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: Chronic stress unleashes an intratumor phage-fibroblast-B cell circuit to promote tumor growthCancer cell · 2026

Summary (written by the submitters)

We performed single-cell RNA sequencing (scRNA-seq) of intratumoral CD45+ Immune cells from mice subjected to chronic unpredictable mild stress (CUMS) or control conditions. Cells were multiplexed using hashtag oligonucleotides (HTO1-HTO4, TotalSeq-C) and sequenced using the 10x Genomics 5-prime Gene Expression + Feature Barcode + B cell receptor (BCR) V(D)J workflow (Well 3).

Read the full summary ↓

This dataset contains GEX profiles of intratumoral B cells from 4 samples (2 conditions x 2 biological replicates; 29,456 cells total). BCR V(D)J sequencing data (IGH/IGK/IGL; 1,107 contigs from 604 B cells) from the same tumor well are also provided. The raw files contain additional unrelated, unlabeled samples as the sequencing was done in multiplex for multiple projects; the processed files reference only the samples used for this study.

Published in

Chronic stress unleashes an intratumor phage-fibroblast-B cell circuit to promote tumor growth

Bashir H, Sanidad KZ, Ravisankar P et al. · Cancer cell 2026 · PMID 42349430 · doi:10.1016/j.ccell.2026.06.004

This dataset

Open GSE327985 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 GSE327985_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 PRJNA1453448 and SRA study SRP691749. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42349430) ↗

Study design

12 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 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.

Samples in this study

GSM9670004 Control mouse 1, mRNA transcript library
GSM9670005 Control mouse 1, VDJ sequencing library
GSM9670006 Control mouse 1, hashtag library
GSM9670007 Control mouse 2, mRNA transcript library
GSM9670008 Control mouse 2, VDJ sequencing library
GSM9670009 Control mouse 2, hashtag library
GSM9670010 CUMS mouse 1, mRNA transcript library
GSM9670011 CUMS mouse 1, VDJ sequencing library
GSM9670012 CUMS mouse 1, hashtag library
GSM9670013 CUMS mouse 2, mRNA transcript library
GSM9670014 CUMS mouse 2, VDJ sequencing library
GSM9670015 CUMS mouse 2, hashtag library

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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.