GEO series

EZH2 alters aggressive variant prostate cancer subtype evolution, but is not required for neuroendocrine prostate cancer. [scRNA-seq]

GSE296986 Mus musculus (mouse) Single-cell RNA-seq 17 samples Submitted 2025/10/28 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: 5 conditions, mostly with about 4 replicates eachGroups 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: EZH2 Suppression Diversifies Prostate Cancer Lineage Variant Evolution and Lacks Efficacy in Inhibiting Disease ProgressionCancer research · 2026

Summary (written by the submitters)

Advanced prostate cancer (PrCa) remains a leading cause of cancer-related death among men because nearly all patients progress on standard therapy that targets androgen receptor (AR) signaling. An important mechanism driving therapeutic resistance is lineage plasticity, the ability of PrCa cells to reprogram into AR independent lineage variants like neuroendocrine (NE) PrCa.

Read the full summary ↓

The histone methyltransferase EZH2 has been implicated in PrCa lineage plasticity and EZH2 inhibitors are being evaluated clinically for the treatment of PrCa. Here we test how Ezh2 impacts the evolution of PrCa lineage plasticity using genetically engineered mice and human patient data. Ezh2 deficiency in mice diversifies the evolution of PrCa lineage variants, including a newly discovered variant with high expression of neurofilament genes. Analogous PrCa lineage variants are detectable in human specimens where they similarly correlate with EZH2 expression. Lineage variant diversification is associated with activation of transcription factor programs and AR cistrome reprogramming that is normally repressed by Ezh2. These findings advance the understanding of PrCa lineage plasticity and have implications for targeting EZH2 as a PrCa therapy.

Published in

EZH2 Suppression Diversifies Prostate Cancer Lineage Variant Evolution and Lacks Efficacy in Inhibiting Disease Progression

Jacobi JJ, Wadosky KM, Jaiswal N et al. · Cancer research 2026 · PMID 41223330 · doi:10.1158/0008-5472.CAN-25-2747

This dataset

Open GSE296986 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 GSE296986_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 PRJNA1262013. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41223330) ↗

Study design

5 conditions, mostly with about 4 replicates each

DKO-EP-DKOE ×4 DKO-M ×4 DKO-EE-DKOE ×3 SKO ×3 TKO-T ×2 DKO ×1

Supports a between-group comparison across 16 samples.

How we read this: 5 replicated groups read from 17 sample titles; they account for 16 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

GSM8981200 DKO-EE-DKOE1393 DKO-EE-DKOE
GSM8981201 DKO-EE-DKOE1223 DKO-EE-DKOE
GSM8981202 DKO-EE-DKOE1232 DKO-EE-DKOE
GSM8981203 DKO-EP-DKOE1219 DKO-EP-DKOE
GSM8981204 DKO-EP-DKOE1221 DKO-EP-DKOE
GSM8981205 DKO-EP-DKOE1546 DKO-EP-DKOE
GSM8981206 DKO-EP-DKOE1562 DKO-EP-DKOE
GSM8981207 DKO-4113
GSM8981208 DKO-M671 DKO-M
GSM8981209 SKO-134 SKO
GSM8981210 SKO-143 SKO
GSM8981211 SKO-159 SKO
GSM8981212 TKO-T2579 TKO-T
GSM8981213 TKO-T1918 TKO-T
GSM8981214 DKO-M361 DKO-M
GSM8981215 DKO-M169 DKO-M
GSM8981216 DKO-M218 DKO-M

Datasets on a similar topic

GSE297143 EZH2 alters aggressive variant prostate cancer subtype evolution, but is not required for neuroendocrine prostate cancer [RNAseq] 54 samples shares ezh2, neuroendocrine, aggressive, evolution, prostate, required, variant
GSE297048 EZH2 alters aggressive variant prostate cancer subtype evolution, but is not required for neuroendocrine prostate cancer [ChIP-seq] 40 samples shares ezh2, neuroendocrine, aggressive, evolution, prostate, required, variant
GSE302602 Dominant negative effects of Weaver syndrome-associated EZH2 variants [RNA-seq] 54 samples shares ezh2, variant
GSE273079 Castration Increases Aggressiveness of Prostatic Luminal Progenitor Cells in Prostate Cancer Through FosL1/AP-1-Mediated Transcriptional Reprogramming 384 samples shares aggressive, prostate
GSE215960 Subclonal evolution revealed by single-cell profiles of expressed mutations identifies adaptation mechanisms to immunotherapy in melanoma [scRNA-seq] 192 samples shares evolution, scrna-seq
GSE271053 A forward genetic screen identifies Sirtuin1 as a driver of neuroendocrine prostate cancer [RNA-Seq] 43 samples shares neuroendocrine, prostate
GSE287166 Molecular Features of Aggressive Preinvasive Lesions driven by Combined MYC Activation and PTEN Loss in Mouse Prostate 21 samples shares aggressive, prostate
GSE274140 Mechanisms by which whole genome doubling drives breast tumor evolution [scRNA-seq] 20 samples shares evolution, scrna-seq

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.