Epigenetic remodeling and 3D chromatin reorganization governed by NKX2-1 drive neuroendocrine prostate cancer
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 206 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
- 206 samples: 205 distinct titles, 1 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
- NKX2-1 drives neuroendocrine transdifferentiation of prostate cancer via epigenetic and 3D chromatin remodelingNature genetics · 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 GSE239278_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 PRJNA998734 and SRA study SRP451561. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 206 sample titles: 205 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.
- GSM7662293 LNCaP, FOXA2-D2 1# ATAC-seq
- GSM7662294 LNCaP, FOXA2-D21 1# ATAC-seq
- GSM7662295 LNCaP, FOXA2-D0 1# ATAC-seq
- GSM7662296 LNCaP, FOXA2-D2 2# ATAC-seq
- GSM7662297 LNCaP, FOXA2-D7 1# ATAC-seq
- GSM7662298 LNCaP, FOXA2-D14 1# ATAC-seq
- GSM7662299 LNCaP, FOXA2-D21 2# ATAC-seq
- GSM7662300 LNCaP, FOXA2-D28 1# ATAC-seq
- GSM7662301 LNCaP, FOXA2-D0 2# ATAC-seq
- GSM7662302 LNCaP, FOXA2-D7 2# ATAC-seq
- GSM7662303 LNCaP, FOXA2-D14 2# ATAC-seq
- GSM7662304 LNCaP, FOXA2-D28 2# ATAC-seq
- GSM7662305 LNCaP, FOXA2-D0, H3K27ac ChIP
- GSM7662306 LNCaP, FOXA2-D2, H3K27ac ChIP
- GSM7662307 LNCaP, FOXA2-D7, sgNC, H3K27ac ChIP
- GSM7662308 LNCaP, FOXA2-D7, sgNKX2-1, H3K27ac ChIP
- GSM7662309 LNCaP, FOXA2-D14, sgNC, H3K27ac ChIP
- GSM7662310 LNCaP, FOXA2-D14, sgNKX2-1, H3K27ac ChIP
- GSM7662311 LNCaP, FOXA2-D21, sgNC, H3K27ac ChIP
- GSM7662312 LNCaP, FOXA2-D21, sgNKX2-1, H3K27ac ChIP
- GSM7662313 LNCaP, FOXA2-D28, sgNC, H3K27ac ChIP
- GSM7662314 LNCaP, FOXA2-D28, sgNKX2-1, H3K27ac ChIP
- GSM7662315 LNCaP, FOXA2-D0, H3K4me1 ChIP
- GSM7662316 LNCaP, FOXA2-D2, H3K4me1 ChIP
- GSM7662317 LNCaP, FOXA2-D7, sgNC, H3K4me1 ChIP
- GSM7662318 LNCaP, FOXA2-D7, sgNKX2-1, H3K4me1 ChIP
- GSM7662319 LNCaP, FOXA2-D14, sgNC, H3K4me1 ChIP
- GSM7662320 LNCaP, FOXA2-D14, sgNKX2-1, H3K4me1 ChIP
- GSM7662321 LNCaP, FOXA2-D21, sgNC, H3K4me1 ChIP
- GSM7662322 LNCaP, FOXA2-D21, sgNKX2-1, H3K4me1 ChIP
- GSM7662323 LNCaP, FOXA2-D28, sgNC, H3K4me1 ChIP
- GSM7662324 LNCaP, FOXA2-D28, sgNKX2-1, H3K4me1 ChIP
- GSM7662325 LNCaP, FOXA2-D0, FOXA2 ChIP
- GSM7662326 LNCaP, FOXA2-D2, FOXA2 ChIP
- GSM7662327 LNCaP, FOXA2-D7, sgNC, FOXA2 ChIP
- GSM7662328 LNCaP, FOXA2-D7, sgNKX2-1, FOXA2 ChIP
- GSM7662329 LNCaP, FOXA2-D14, sgNC, FOXA2 ChIP
- GSM7662330 LNCaP, FOXA2-D14, sgNKX2-1,FOXA2 ChIP
- GSM7662331 LNCaP, FOXA2-D21, sgNC, FOXA2 ChIP
- GSM7662332 LNCaP, FOXA2-D21, sgNKX2-1,FOXA2 ChIP
+ 166 more — browse all 206 samples with per-sample file links →
- GSE115501 RNA sequencing on circulating tumor cells from prostate cancer patients 136 samples same disease briefing · shares 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
- GSE210848 Lineage specific chromatin modification guides Pax5 mediated gene expression in neuroendocrine like differentiation of prostate cancer 32 samples shares neuroendocrine, chromatin, prostate
- GSE255154 Epigenetic disruption of the RARgamma complex impairs its function to bookmark AR enhancer interactions required for enzalutamide sensitivity in prostate cancer 139 samples shares epigenetic, 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.