RARg bookmarking functions in prostate cancer (CUT&RUN)
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 98 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
- 98 samples: 98 samples, each with a distinct title — no replicated groupsGroups 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.
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 GSE255386_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 PRJNA1074790 and SRA study SRP488992. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 98 sample titles: 98 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.
- GSM8070953 Mock.M.AR.1.sorted.rmdup.BAM
- GSM8070954 Mock.M.AR.2.sorted.rmdup.BAM
- GSM8070955 Mock.M.AR.3.sorted.rmdup.BAM
- GSM8070956 Mock.DHT.AR.1.sorted.rmdup.BAM
- GSM8070957 Mock.DHT.AR.2.sorted.rmdup.BAM
- GSM8070958 Mock.DHT.AR.3.sorted.rmdup.BAM
- GSM8070959 Mock.M.K3.1.sorted.rmdup.BAM
- GSM8070960 Mock.M.K3.2.sorted.rmdup.BAM
- GSM8070961 Mock.M.K3.3.sorted.rmdup.BAM
- GSM8070962 Mock.DHT.K3.1.sorted.rmdup.BAM
- GSM8070963 Mock.DHT.K3.2.sorted.rmdup.BAM
- GSM8070964 Mock.DHT.K3.3.sorted.rmdup.BAM
- GSM8070965 RARg.M.IgG.1.sorted.rmdup.BAM
- GSM8070966 RARg.M.IgG.2.sorted.rmdup.BAM
- GSM8070967 RARg.M.IgG.3.sorted.rmdup.BAM
- GSM8070968 RARg.DHT.AR.1.sorted.rmdup.BAM
- GSM8070969 RARg.DHT.AR.2.sorted.rmdup.BAM
- GSM8070970 RARg.DHT.AR.3.sorted.rmdup.BAM
- GSM8070971 RARg.M.AR.1.sorted.rmdup.BAM
- GSM8070972 RARg.M.AR.2.sorted.rmdup.BAM
- GSM8070973 RARg.M.AR.3.sorted.rmdup.BAM
- GSM8070974 RARg.CD.RARg.1.sorted.rmdup.BAM
- GSM8070975 RARg.CD.RARg.2.sorted.rmdup.BAM
- GSM8070976 RARg.CD.RARg.3.sorted.rmdup.BAM
- GSM8070977 RARg.M.RARg.1.sorted.rmdup.BAM
- GSM8070978 RARg.M.RARg.2.sorted.rmdup.BAM
- GSM8070979 RARg.M.RARg.3.sorted.rmdup.BAM
- GSM8070980 RARg.M.K3.1.sorted.rmdup.BAM
- GSM8070981 RARg.M.K3.2.sorted.rmdup.BAM
- GSM8070982 RARg.M.K3.3.sorted.rmdup.BAM
- GSM8070983 RARg.DHT.K3.1.sorted.rmdup.BAM
- GSM8070984 RARg.DHT.K3.2.sorted.rmdup.BAM
- GSM8070985 RARg.DHT.K3.3.sorted.rmdup.BAM
- GSM8070986 RARg.CD.K3.1.sorted.rmdup.BAM
- GSM8070987 RARg.CD.K3.2.sorted.rmdup.BAM
- GSM8070988 RARg.CD.K3.3.sorted.rmdup.BAM
- GSM8070989 TACC1.RARg.M.AR.3.sorted.rmdup.BAM
- GSM8070990 TACC1.RARg.M.AR.1.sorted.rmdup.BAM
- GSM8070991 TACC1.RARg.M.AR.2.sorted.rmdup.BAM
- GSM8070992 TACC1.RARg.DHT.AR.3.sorted.rmdup.BAM
+ 58 more — browse all 98 samples with per-sample file links →
- GSE242541 ONECUT2 is a druggable driver of luminal to basal breast cancer plasticity 12 samples same disease briefing · shares cut
- 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
- GSE303343 A unified network systems approach uncovers a core program underlying T follicular helper cell differentiation [CUT&RUN] 48 samples shares cut, run
- GSE287902 BPTF regulstes androgen receptor activity by enhancing chromatin accessibility and stabilizing the AR-FOXA1 interaction [Cut&Run] 40 samples shares cut, run
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.