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Study of CPI-0209 in patients with advanced tumors.

GSE176490 Homo sapiens (human) RNA-seq (gene expression) 106 samples Submitted 2024/06/26 Platform GPL20301
At a glance

RNA-seq (gene expression) · human · 106 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)
Samples
106 samples: 32 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.
Paper
Comprehensive Target Engagement by the EZH2 Inhibitor Tulmimetostat Allows for Targeting of ARID1A Mutant CancersCancer research · 2024
Summary (written by the submitters)
Advanced bladder cancer remains a difficult cancer to treat, and for the majority of patients, current standard treatments ultimately prove ineffective. These tumors frequently harbor mutations in the BAF complex subunit ARID1A, which has been reported to confer sensitivity to EZH2 inhibition in several tumor types. Here we describe the generation of CPI-0209, a best-in-class, orally available EZH2 inhibitor.
Read the full summary ↓
We show that mutant bladder cancer lines harboring ARID1A loss of function (LOF) mutations are preferentially sensitive to inhibition of EZH2. Treatment with CPI-0209 not only elicits a significant monotherapeutic response in ARID1A mutant models, it also outperforms cisplatin and improves response in chemo-resistant models. These findings shine light on new therapeutic opportunities for patients with advanced urothelial carcinoma.
Published in
Comprehensive Target Engagement by the EZH2 Inhibitor Tulmimetostat Allows for Targeting of ARID1A Mutant Cancers
Keller PJ, Adams EJ, Wu R et al. · Cancer research 2024 · PMID 38833522 · doi:10.1158/0008-5472.CAN-24-0398
This dataset
Open GSE176490 in finder → Find more human RNA-seq datasets →
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 GSE176490_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 PRJNA736432 and SRA study SRP323411. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38833522) ↗
Study design
32 conditions, mostly in duplicate
PT5-MT Cycle 1 Day ×4 PT6-MT Cycle 1 Day ×4 PT10-MT Cycle 1 Day ×4 PT12-MT Cycle 1 Day ×4 PT13-MT Cycle 1 Day ×4 PT21-MT Cycle 1 Day ×4 PT22-MT Cycle 1 Day ×4 PT24-MT Cycle 1 Day ×4 +38 more

Supports a between-group comparison across 92 samples.

How we read this: 32 replicated groups read from 106 sample titles; they account for 92 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

+ 66 more — browse all 106 samples with per-sample file links →

Datasets on a similar topic

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