GEO series

Bulk RNA sequencing of prostate cancer (PCa) primary tumors and metastases: Epworth Clinical Cohort

GSE339157 Homo sapiens (human) Single-cell RNA-seq 48 samples Submitted 2026/07/31 Platform GPL21290

At a glance

Single-cell RNA-seq · human · 48 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Topic: Prostate cancerThis series is part of our curated briefing on it.
Samples: 48 samples: 6 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.

Summary (written by the submitters)

Prostate cancer (PCa) frequently metastasizes to bone, marking incurable disease. This progression is driven by an immunologically cold bone tumor microenvironment that fosters resistance to therapy. To define the mechanisms underlying this uniquely immunosuppressive niche, we applied spatial single cell analyses across primary tumors and metastatic sites.

Read the full summary ↓

Bone metastases showed marked suppression of tumor-intrinsic type I interferon (IFN-I) signaling and loss of antigen presentation, features that strongly predicted reduced bone metastasis-free survival. Tumor-intrinsic IFN-I expression correlated with memory T cell infiltration, whereas the bone myeloid compartment was enriched for protumor macrophages and showed reduced dendritic cell (DC) activation and antigen presentation. Digital spatial profiling of matched tumors revealed a broad loss of IFN-I-regulated immunostimulatory and checkpoint molecules. Notably, B7-H3, a putative negative regulator of IFN-I, was highly expressed in bone metastases and inversely associated with antigen presentation. These findings define bone-specific mechanisms of immune resistance and highlight therapeutic vulnerabilities that could inform precision strategies for PCa.

This dataset

Open GSE339157 in finder → Find more human RNA-seq datasets → Prostate cancer landscape →

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 GSE339157_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 PRJNA1497887 and SRA study SRP719553. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly with about 4 replicates each

Primary PCa, patient with bone-metastatic dis… ×14 Primary PCa, patient with no bone metastasis,… ×11 PCa bone metastases, donor RC ×11 Primary PCa, patient with bone-metastatic dis… ×4 PCa lymph node metastases, donor RC ×4 Primary PCa, patient with no bone metastasis,… ×4

Supports a between-group comparison across 48 samples.

How we read this: 6 replicated groups read from 48 sample titles; they account for 48 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

GSM9889511 Primary PCa, patient with bone-metastatic disease, donor NR_01 Primary PCa, patient wi…
GSM9889512 Primary PCa, patient with no bone metastasis, donor NR_02 Primary PCa, patient wi…
GSM9889513 Primary PCa, patient with no bone metastasis, donor NR_03 Primary PCa, patient wi…
GSM9889514 Primary PCa, patient with no bone metastasis, donor NR_04 Primary PCa, patient wi…
GSM9889515 Primary PCa, patient with bone-metastatic disease, donor NR_05 Primary PCa, patient wi…
GSM9889516 Primary PCa, patient with no bone metastasis, donor NR_06 Primary PCa, patient wi…
GSM9889517 Primary PCa, patient with no bone metastasis, donor NR_07 Primary PCa, patient wi…
GSM9889518 Primary PCa, patient with bone-metastatic disease, donor NR_08 Primary PCa, patient wi…
GSM9889519 Primary PCa, patient with bone-metastatic disease, donor NR_09 Primary PCa, patient wi…
GSM9889520 Primary PCa, patient with no bone metastasis, donor NR_10 Primary PCa, patient wi…
GSM9889521 Primary PCa, patient with no bone metastasis, donor NR_11 Primary PCa, patient wi…
GSM9889522 Primary PCa, patient with no bone metastasis, donor NR_12 Primary PCa, patient wi…
GSM9889523 Primary PCa, patient with no bone metastasis, donor NR_13 Primary PCa, patient wi…
GSM9889524 Primary PCa, patient with no bone metastasis, donor NR_14 Primary PCa, patient wi…
GSM9889525 Primary PCa, patient with no bone metastasis, donor NR_15 Primary PCa, patient wi…
GSM9889526 PCa bone metastases, donor RC_01 PCa bone metastases, do…
GSM9889527 PCa bone metastases, donor RC_02 PCa bone metastases, do…
GSM9889528 PCa bone metastases, donor RC_03 PCa bone metastases, do…
GSM9889529 Primary PCa, patient with bone-metastatic disease, donor RC_03 Primary PCa, patient wi…
GSM9889530 Primary PCa, patient with bone-metastatic disease, donor RC_04 Primary PCa, patient wi…
GSM9889531 PCa bone metastases, donor RC_05 PCa bone metastases, do…
GSM9889532 Primary PCa, patient with bone-metastatic disease, donor RC_05 Primary PCa, patient wi…
GSM9889533 PCa bone metastases, donor RC_06 PCa bone metastases, do…
GSM9889534 Primary PCa, patient with bone-metastatic disease, donor RC Primary PCa, patient wi…
GSM9889535 Primary PCa, patient with bone-metastatic disease, donor RC_07 Primary PCa, patient wi…
GSM9889536 PCa bone metastases, donor RC_08 PCa bone metastases, do…
GSM9889537 PCa bone metastases, donor RC_09 PCa bone metastases, do…
GSM9889538 PCa bone metastases, donor RC_10 PCa bone metastases, do…
GSM9889539 Primary PCa, patient with bone-metastatic disease, donor RC_11 Primary PCa, patient wi…
GSM9889540 PCa bone metastases, donor RC_12 PCa bone metastases, do…
GSM9889541 PCa bone metastases, donor RC_13 PCa bone metastases, do…
GSM9889542 PCa lymph node metastases, donor RC_15 PCa lymph node metastas…
GSM9889543 PCa bone metastases, donor RC_15 PCa bone metastases, do…
GSM9889544 Primary PCa, patient with bone-metastatic disease, donor RC_15 Primary PCa, patient wi…
GSM9889545 PCa lymph node metastases, donor RC_18 PCa lymph node metastas…
GSM9889546 Primary PCa, patient with bone-metastatic disease, donor RC_16 Primary PCa, patient wi…
GSM9889547 Primary PCa, patient with no bone metastasis, donor RC_18 Primary PCa, patient wi…
GSM9889548 Primary PCa, patient with no bone metastasis, donor RC_19 Primary PCa, patient wi…
GSM9889549 Primary PCa, patient with bone-metastatic disease, donor RC_20 Primary PCa, patient wi…
GSM9889550 Primary PCa, patient with bone-metastatic disease, donor RC_21 Primary PCa, patient wi…

+ 8 more — browse all 48 samples with per-sample file links →

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Search all human 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.