Epigenomic profiling of circulating chromatin to detect and monitor squamous transformation in prostate cancer
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 12 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Topic
- Prostate cancerThis series is part of our curated briefing on it.
- Samples
- 12 samples: 10 distinct titles, 2 of them repeatedGroups 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
- Plasma epigenomic profiling reveals treatment-emergent squamous transformation in prostate cancerNPJ precision oncology · 2025
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE291318_RAW.tar (it can run to tens of gigabytes).
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.
What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1232815 and SRA study SRP568523. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 12 sample titles: 10 distinct titles with little repetition. 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.
- GSM8833398 JC_K27_SCPC_RGENP3649
- GSM8833399 JC_K4_reSCPC_RGENP3649
- GSM8833400 JC_K27_SCPC_GENP8956
- GSM8833401 JC_K4_SCPC_GENP8956
- GSM8833402 JC_K27_SCPC_RGENP4611
- GSM8833403 JC_K4_reSCPC_RGENP4611
- GSM8833404 JC_K27_SquamousPC_FL
- GSM8833405 JC_K4_SquamousPC_FL
- GSM8833406 wHS_RGENP3649_Squamous
- GSM8833407 wHS_GENP8956_Squamous
- GSM8833408 wHS_RGENP4611_Squamous
- GSM8833409 wHS_Squamous_Cell_PC_MLF
- GSE115501 RNA sequencing on circulating tumor cells from prostate cancer patients 136 samples same disease briefing · shares circulating, prostate
- GSE222467 The RNA binding proteins LARP4A and LARP4B promote tumour growth and metastasis in prostate cancer and osteosarcoma 12 samples same disease briefing · shares prostate
- GSE300947 A novel six-biomarker panel identified from male breast cancer-associated fibroblasts demonstrates prognostic power for prostate tumors 6 samples same disease briefing · shares prostate
- GSE120181 Human prostate cancer cell line, 22Rv1: Control vs. luteolin treatment 2 samples same disease briefing · shares prostate
- GSE71008 Plasma extracellular RNA profiles in healthy and cancer patients 192 samples same disease briefing
- GSE242541 ONECUT2 is a druggable driver of luminal to basal breast cancer plasticity 12 samples same disease briefing
- GSE282760 Epigenomic manipulation reveals the relationship between locus specific chromatin dynamics and gene expression [ChIP-seq] 36 samples shares epigenomic, chromatin
- GSE210848 Lineage specific chromatin modification guides Pax5 mediated gene expression in neuroendocrine like differentiation of prostate cancer 32 samples shares chromatin, prostate
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.