GEO series

Genome-scale DNA methylome and transcriptome profiles of early prostate cancer recurrence after prostatectomy [RNA-seq]

GSE278135 Homo sapiens (human) DNA methylation 18 samples Submitted 2025/03/23 Platform GPL24676

At a glance

DNA methylation · human · 18 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Homo sapiens (human)
Topic: Prostate cancerThis series is part of our curated briefing on it.
Samples: 18 samples: 8 × Prostate tumour Biochemical recurrence RNA-seq, Patient vs 7 × Prostate tumour No biochemical recurrence RNA-seq, PatientGroups 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) is a major health burden world-wide and despite early treatment, a very large proportion of patients present with biochemical recurrence (BCR) post-treatment, reflected by a rise in PSA over a clinical threshold. Novel transcriptomic and epigenomic biomarkers can provide a powerful tool for clinical management of PCa.

Read the full summary ↓

Here we provide matched RNA-Sequencing and array-based genome-wide DNA methylome data of PCa patients (n = 17) with, or without, evidence of BCR following early radical prostatectomy. We have utilized Formalin-Fixed Paraffin-Embedded tissues to generate this data and included technical replicates to provide further validity of the data. We describe the sample features, experimental design, methods and bioinformatic pipeline for processing these multi-omic data. Importantly, we provide comprehensive clinical, histopathological, and follow-up data for each patient to enable correlating transcriptome and methylome features with clinical features. Our data will contribute towards the efforts of developing epigenomic and transcriptomic markers for BCR and also facilitate a deeper understanding of the molecular basis of PCa recurrence.

This dataset

Open GSE278135 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 GSE278135_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: Look for beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA1165752 and SRA study SRP535013. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

8 × Prostate tumour Biochemical recurrence RNA-seq, Patient vs 7 × Prostate tumour No biochemical recurrence RNA-seq, Patient

Supports a between-group comparison across 15 samples.

How we read this: 2 replicated groups read from 18 sample titles; they account for 15 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

GSM8540645 Prostate tumour Biochemical persistence RNA-seq, Patient 1
GSM8540646 Prostate tumour Biochemical recurrence RNA-seq, Patient 2 Prostate tumour Biochem…
GSM8540647 Prostate tumour No biochemical recurrence RNA-seq, Patient 3 Prostate tumour No bioc…
GSM8540648 Prostate tumour Biochemical recurrence RNA-seq, Patient 4 Prostate tumour Biochem…
GSM8540649 Prostate tumour Biochemical recurrence RNA-seq, Patient 5 Prostate tumour Biochem…
GSM8540650 Prostate tumour Biochemical recurrence RNA-seq, Patient 6 Prostate tumour Biochem…
GSM8540651 Prostate tumour Biochemical recurrence RNA-seq, Patient 7 Prostate tumour Biochem…
GSM8540652 Prostate tumour Biochemical recurrence RNA-seq, Patient 8 Prostate tumour Biochem…
GSM8540653 Prostate tumour No biochemical recurrence RNA-seq, Patient 9 Prostate tumour No bioc…
GSM8540654 Prostate tumour No biochemical recurrence RNA-seq, Patient 10 Prostate tumour No bioc…
GSM8540655 Prostate tumour No biochemical recurrence RNA-seq, Patient 11 Prostate tumour No bioc…
GSM8540656 Prostate tumour No biochemical recurrence RNA-seq, Patient 12 Prostate tumour No bioc…
GSM8540657 Prostate tumour Biochemical recurrence RNA-seq, Patient 13 Prostate tumour Biochem…
GSM8540658 Prostate tumour No biochemical recurrence RNA-seq, Patient 14, Repicate 1
GSM8540659 Prostate tumour No biochemical recurrence RNA-seq, Patient 14, Replicate 2
GSM8540660 Prostate tumour Biochemical recurrence RNA-seq, Patient 15 Prostate tumour Biochem…
GSM8540661 Prostate tumour No biochemical recurrence RNA-seq, Patient 16 Prostate tumour No bioc…
GSM8540662 Prostate tumour No biochemical recurrence RNA-seq, Patient 17 Prostate tumour No bioc…

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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.