The estrogen and androgen responses in the immortalized human prostate cancer cell line VCaP
RNA-seq (gene expression) · human · 12 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Topic
- Prostate cancerThis series is part of our curated briefing on it.
- Samples
- 12 samples: 3 × VCaP, Control, vs 3 × VCaP, Estradiol, vs 3 × VCaP, Estradiol + R1881, vs 3 × VCaP, R1881,Groups 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
- The estrogen signaling pathway reprograms prostate cancer cell metabolism and supports proliferation and disease progressionThe Journal of clinical investigation · 2024
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 GSE256370_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1079289 and SRA study SRP491108. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8096344 VCaP, Control, rep 1 VCaP, Control,
- GSM8096345 VCaP, Control, rep 2 VCaP, Control,
- GSM8096346 VCaP, Control, rep 3 VCaP, Control,
- GSM8096347 VCaP, Estradiol, rep 1 VCaP, Estradiol,
- GSM8096348 VCaP, Estradiol, rep 2 VCaP, Estradiol,
- GSM8096349 VCaP, Estradiol, rep 3 VCaP, Estradiol,
- GSM8096350 VCaP, Estradiol + R1881, rep 1 VCaP, Estradiol + R1881,
- GSM8096351 VCaP, Estradiol + R1881, rep 2 VCaP, Estradiol + R1881,
- GSM8096352 VCaP, Estradiol + R1881, rep 3 VCaP, Estradiol + R1881,
- GSM8096353 VCaP, R1881, rep 1 VCaP, R1881,
- GSM8096354 VCaP, R1881, rep 2 VCaP, R1881,
- GSM8096355 VCaP, R1881, rep 3 VCaP, R1881,
- GSE120181 Human prostate cancer cell line, 22Rv1: Control vs. luteolin treatment 2 samples same disease briefing · shares prostate, line
- 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
- GSE242541 ONECUT2 is a druggable driver of luminal to basal breast cancer plasticity 12 samples same disease briefing
- GSE71008 Plasma extracellular RNA profiles in healthy and cancer patients 192 samples same disease briefing
- GSE157605 RNA sequencing data of PC3, an androgen negative human prostate cell line, treated with estrogenic compounds 12 samples shares estrogen, androgen, prostate, line
- GSE222196 Treatment of prostate cancer cell lines with Androgen Receptor and Receptor Tyrosine Kinase inhibitors 246 samples shares androgen, prostate, line
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.