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Gene expression profile using Rhapsody/scRNA-seq of brain metastasis-associated immune cells.

GSE228379 Mus musculus (mouse) Single-cell RNA-seq 17 samples Submitted 2024/08/26 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 17 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
17 samples: 9 × Brain from mouse with silibinin (STAT3 inhibitor) # vs 8 × Brain from mouse with vehicle #Groups 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
TIMP1 Mediates Astrocyte-Dependent Local Immunosuppression in Brain Metastasis Acting on Infiltrating CD8+ T CellsCancer discovery · 2025
Summary (written by the submitters)
We used BD Rhapsody™/scRNA-seq to analyze the heterogeneity of lymphocytes in brain metastasis
Published in
TIMP1 Mediates Astrocyte-Dependent Local Immunosuppression in Brain Metastasis Acting on Infiltrating CD8+ T Cells
Priego N, de Pablos-Aragoneses A, Perea-García M et al. · Cancer discovery 2025 · PMID 39354883 · doi:10.1158/2159-8290.CD-24-0134
This dataset
Open GSE228379 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 GSE228379_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 PRJNA949600 and SRA study SRP429752. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39354883) ↗
Study design
9 × Brain from mouse with silibinin (STAT3 inhibitor) # vs 8 × Brain from mouse with vehicle #

Supports a between-group comparison across 17 samples.

How we read this: 2 replicated groups read from 17 sample titles; they account for 17 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 mouse RNA-seq datasets in GEO →

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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.