GEO series

Single-cell transcriptomes of subcutaneous and orthotopic RM-1 mouse prostate tumors collected 7 days after sham or irreversible electroporation

GSE341190 Mus musculus (mouse) Single-cell RNA-seq 10 samples Submitted 2026/08/01 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 10 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: 10 samples: 3 × Single-cell RNA-seq of subcutaneous RM-1 tumor, sham-treated, vs 3 × Single-cell RNA-seq of subcutaneous RM-1 tumor, IRE-treated, vs 2 × Single-cell RNA-seq of orthotopic RM-1 prostate tumor, sham-treated, vs 2 × Single-cell RNA-seq of orthotopic RM-1 prostate tumor, IRE-treated,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.

Summary (written by the submitters)

This submission describes a single-cell RNA-sequencing resource generated from two mouse prostate cancer models. The dataset contains six subcutaneous RM-1 tumors and four orthotopic RM-1 prostate tumors collected 7 days after sham intervention or irreversible electroporation (IRE). Each excised tumor represents one biological replicate and was processed as an independent whole-cell suspension before library construction.

Read the full summary ↓

Raw sequencing reads were previously submitted to SRA under BioProject PRJNA1497318 and are linked here through the corresponding SRA accessions. The GEO submission provides the processed filtered gene-barcode matrices used for downstream quality control, integration, clustering, and cell-type annotation.

This dataset

Open GSE341190 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 GSE341190_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 PRJNA1497318 and SRA study SRP719304. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × Single-cell RNA-seq of subcutaneous RM-1 tumor, sham-treated, vs 3 × Single-cell RNA-seq of subcutaneous RM-1 tumor, IRE-treated, vs 2 × Single-cell RNA-seq of orthotopic RM-1 prostate tumor, sham-treated, vs 2 × Single-cell RNA-seq of orthotopic RM-1 prostate tumor, IRE-treated,

Supports a between-group comparison across 10 samples.

How we read this: 4 replicated groups read from 10 sample titles; they account for 10 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

GSM9901661 Single-cell RNA-seq of subcutaneous RM-1 tumor, sham-treated, biological replicate 1 Single-cell RNA-seq of …
GSM9901662 Single-cell RNA-seq of subcutaneous RM-1 tumor, sham-treated, biological replicate 2 Single-cell RNA-seq of …
GSM9901663 Single-cell RNA-seq of subcutaneous RM-1 tumor, sham-treated, biological replicate 3 Single-cell RNA-seq of …
GSM9901664 Single-cell RNA-seq of subcutaneous RM-1 tumor, IRE-treated, biological replicate 1 Single-cell RNA-seq of …
GSM9901665 Single-cell RNA-seq of subcutaneous RM-1 tumor, IRE-treated, biological replicate 2 Single-cell RNA-seq of …
GSM9901666 Single-cell RNA-seq of subcutaneous RM-1 tumor, IRE-treated, biological replicate 3 Single-cell RNA-seq of …
GSM9901667 Single-cell RNA-seq of orthotopic RM-1 prostate tumor, sham-treated, biological replicate 1 Single-cell RNA-seq of …
GSM9901668 Single-cell RNA-seq of orthotopic RM-1 prostate tumor, sham-treated, biological replicate 2 Single-cell RNA-seq of …
GSM9901669 Single-cell RNA-seq of orthotopic RM-1 prostate tumor, IRE-treated, biological replicate 1 Single-cell RNA-seq of …
GSM9901670 Single-cell RNA-seq of orthotopic RM-1 prostate tumor, IRE-treated, biological replicate 2 Single-cell RNA-seq of …

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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.