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Effects of CDK8/19 Mediator Kinase inhibition on gene expression in castration-resistant prostate cancer cell line 22Rv1 and its derivatives grown in vitro.

GSE240369 Homo sapiens (human) RNA-seq (gene expression) 48 samples Submitted 2024/03/31 Platform GPL24676Platform GPL20301
At a glance

RNA-seq (gene expression) · human · 48 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
48 samples: 16 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
Mediator kinase inhibition reverses castration resistance of advanced prostate cancerThe Journal of clinical investigation · 2024
Summary (written by the submitters)
RNA-Seq analysis was carried out to investigate the effects of selective CDK8/19 inhibitor SNX631 on gene expression in different 22RV1 derivatives grown in cell culture, under androgen-supplemented and androgen-deprived conditions. The 22Rv1 derivatives were generated as following: Parental 22Rv1 (Rv1-WT) were transduced with a lentivirus expressing luciferase, yielding the derivative Rv1-Luc.
Read the full summary ↓
22Rv1 cells with a double knockout of CDK8 and CDK19 (Rv1-dKO) were made via CRISPR/Cas9. Rv1-dKO cells were further transduced with lentiviruses to generate Rv1-dKO re-expression derivatives that express wild-type CDK8 or CDK19 (Rv1-dKO-CDK8 or Rv1-dKO-CDK19) and kinase-inactive D173A mutants (Rv1-dKO-CDK8M or Rv1-dKO-CDK19M).
Published in
Mediator kinase inhibition reverses castration resistance of advanced prostate cancer
Li J, Hilimire TA, Liu Y et al. · The Journal of clinical investigation 2024 · PMID 38546787 · doi:10.1172/JCI176709
This dataset
Open GSE240369 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 GSE240369_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 PRJNA1003453 and SRA study SRP454049. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38546787) ↗
Study design
16 conditions, mostly in triplicate
Rv1_WT_FBS_Ctrl_3d ×3 Rv1_WT_FBS_SNX631_3d ×3 Rv1_WT_CSS_Ctrl_3d ×3 Rv1_WT_CSS_SNX631_3d ×3 Rv1_Luc_FBS_Ctrl_3d ×3 Rv1_Luc_FBS_SNX631_3d ×3 Rv1_Luc_CSS_Ctrl_3d ×3 Rv1_Luc_CSS_SNX631_3d ×3 +8 more

Supports a between-group comparison across 48 samples.

How we read this: 16 replicated groups read from 48 sample titles; they account for 48 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

+ 8 more — browse all 48 samples with per-sample file links →

More Prostate cancer datasets

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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.