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RNA-seq analysis of global gene expression changes in human FSHD immortalized myotubes following treatment with the BAZ1A inhibitor C06

GSE334189 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2026/06/10 Platform GPL20301
At a glance

RNA-seq (gene expression) · human · 18 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
18 samples: 5 × 15Ai_untreatment vs 5 × 15Ai_DMSO vs 4 × 15Ai_C06-100nM vs 4 × 15Ai_C06-500nMGroups 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)
Facioscapulohumeral muscular dystrophy (FSHD) is caused by epigenetic dysregulation of the disease locus, leading to pathogenic misexpression of DUX4 in skeletal muscle. We identified BAZ1A (bromodomain adjacent to zinc finger domain protein 1A) as a promising target for FSHD therapeutic development, and identified a small-molecule compound termed C06 that binds BAZ1A in vitro and is a potent repressor of DUX4.
Read the full summary ↓
To determine the global specificity of C06 activity, we performed RNA-seq on FSHD myotubes treated with different concentrations of C06, and compared the gene expression profiles. At low concentrations, C06 returns the DUX4 gene expression signature to a healthier profile without major effects on the muscle transcriptome. Thus, C06 is a useful tool for potent and specific DUX4 suppression, and a viable candidate for further development.
This dataset
Open GSE334189 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 GSE334189_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 PRJNA1474300 and SRA study SRP706348. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 × 15Ai_untreatment vs 5 × 15Ai_DMSO vs 4 × 15Ai_C06-100nM vs 4 × 15Ai_C06-500nM

Supports a between-group comparison across 18 samples.

How we read this: 4 replicated groups read from 18 sample titles; they account for 18 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
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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.