Matrix stiffness modulates androgen response genes and chromatin state in prostate cancer
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 15 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
- 15 samples: 6 conditions, mostly in triplicateGroups 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
- Matrix stiffness modulates androgen response genes and chromatin state in prostate cancerNAR cancer · 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 GSE272029_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 PRJNA1134682 and SRA study SRP519555. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 6 replicated groups read from 15 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.
- GSM8391377 C42B_ATAC_plastic_rep1 C42B_ATAC_plastic
- GSM8391378 C42B_ATAC_plastic_rep2 C42B_ATAC_plastic
- GSM8391379 C42B_ATAC_50kPa_rep1 C42B_ATAC_50kPa
- GSM8391380 C42B_ATAC_50kPa_rep2 C42B_ATAC_50kPa
- GSM8391381 C42B_ATAC_0.5kPa_rep1 C42B_ATAC_0.5kPa
- GSM8391382 C42B_ATAC_0.5kPa_rep2 C42B_ATAC_0.5kPa
- GSM8391383 C42B_RNA_plastic_rep1 C42B_RNA_plastic
- GSM8391384 C42B_RNA_plastic_rep2 C42B_RNA_plastic
- GSM8391385 C42B_RNA_plastic_rep3 C42B_RNA_plastic
- GSM8391386 C42B_RNA_50kPa_rep1 C42B_RNA_50kPa
- GSM8391387 C42B_RNA_50kPa_rep2 C42B_RNA_50kPa
- GSM8391388 C42B_RNA_50kPa_rep3 C42B_RNA_50kPa
- GSM8391389 C42B_RNA_0.5kPa_rep1 C42B_RNA_0.5kPa
- GSM8391390 C42B_RNA_0.5kPa_rep2 C42B_RNA_0.5kPa
- GSM8391391 C42B_RNA_0.5kPa_rep3 C42B_RNA_0.5kPa
- GSE115501 RNA sequencing on circulating tumor cells from prostate cancer patients 136 samples same disease briefing · shares prostate, state
- 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, state
- 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, state
- GSE120181 Human prostate cancer cell line, 22Rv1: Control vs. luteolin treatment 2 samples same disease briefing · shares prostate, state
- 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
- GSE210848 Lineage specific chromatin modification guides Pax5 mediated gene expression in neuroendocrine like differentiation of prostate cancer 32 samples shares chromatin, prostate, state
- GSE339459 5β-Dihydrotestosterone and mutant androgen receptor vulnerability in prostate cancer 30 samples shares androgen, prostate, state
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.