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Comprehensive target engagement by EZH2 inhibitor CPI-0209 allows for preferential targeting of ARID1A mutant urothelial carcinoma

GSE176493 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 252 samples Submitted 2024/06/26 Platform GPL20301Platform GPL18573
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 252 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
Bladder cancerThis series is part of our curated briefing on it.
Samples
252 samples: 72 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
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
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 GSE176493 in finder → Find more human RNA-seq datasets → Bladder 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 GSE176493_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA736424 and SRA study SRP323193. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38833522) ↗
Study design
72 conditions, mostly in duplicate
HT1376-TetOn-ARID1A_DMSO_with Dox_SMARCA4 ×4 HT1376-TetOn_CPI-0209_with Dox_SMARCA4 ×4 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 +119 more

Supports a between-group comparison across 197 samples.

How we read this: 72 replicated groups read from 252 sample titles; they account for 197 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

+ 212 more — browse all 252 samples with per-sample file links →

More Bladder 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.