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Androgen Deprivation Alters the Transcriptome of Endothelial Cells More Dramatically in Human Prostate Cancer Tissue than in Benign Prostate Tissue

GSE168292 Homo sapiens (human) RNA-seq (gene expression) 127 samples Submitted 2024/03/03 Platform GPL16791
At a glance

RNA-seq (gene expression) · human · 127 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
127 samples: 34 conditions, mostly in duplicateGroups 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.
Summary (written by the submitters)
Purpose: Examine the cell type specific (Epithelial, Endothelial, and Stromal) transcriptome profile between prostate primary tissue xenografts of prostate tissue tumor tissue and uninvolved tissue (named non-tumor hereafter) in response testosterone (T) deprivation. Additional cell type specific untreated fresh tissue from both tumor and non-tumor samples is included for additional validation.
Read the full summary ↓
Related samples previously uploaded to GEO are found under accession number GSE145641. Method: Nude-Fox1nu mice were castrated and silastic tubing containing dry T was inserted providing “humanized” levels of circulating T. 5-8 pieces of fresh human prostate tissue was then inserted subcutaneously along the flank of the animal. For samples not subjected to T-deprivation, after 30 days the animal was euthanized, and tissue was harvested. For samples undergoing T-deprivation, after 30 days with humanized circulating T levels, T-deprivation was performed by surgical removal of silastic tubing after which serum T levels dropped below the level of detection within 24 hours. Samples were then harvested at Pre T-deprivation time point, an early T-deprivation time point (3-days) or late T-deprivation timepoint (15-17 days) post-surgery. Tissue from fresh human prostate or tissue from xenograft and was then enriched into endothelial, epithelial and the remaining stromal compartments using magnetic bead enrichment. RNA-Seq was then preformed on cell types from both origins and the results compared to determine the cell type specific effects of T-deprivation on the human prostate transcriptome.
This dataset
Open GSE168292 in finder → Find more human RNA-seq datasets → Prostate cancer landscape →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE168292_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA706900 and SRA study SRP309441. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
34 conditions, mostly in duplicate
HP1167-T-Endo-Xen-Post-D ×3 HP1167-T-Stroma-Xen-Post-D ×3 HP1125-NT-Endo-Xen-Post-D ×2 HP1125-NT-Epi-Xen-Post-D ×2 HP1131-NT-Endo-Xen-Post-D ×2 HP1131-NT-Epi-Xen-Post-D ×2 HP1125-NT-Stroma-Xen-Post-D ×2 HP1131-NT-Stroma-Xen-Post-D ×2 +83 more

Supports a between-group comparison across 70 samples.

How we read this: 34 replicated groups read from 127 sample titles; they account for 70 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.

Samples in this study

+ 87 more — browse all 127 samples with per-sample file links →

More Prostate cancer datasets

Search all human RNA-seq datasets in GEO →

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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.