GEO series

Longitudinal measures of RNA expression and disease activity in FSHD muscle biopsies

GSE140261 Homo sapiens (human) RNA-seq (gene expression) 35 samples Submitted 2020/02/25 Platform GPL16791

At a glance

RNA-seq (gene expression) · human · 35 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: 35 samples
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)

Advances in understanding the pathophysiology of facioscapulohumeral dystrophy (FSHD) have led to the discovery of candidate therapeutics and it is important to identify markers of disease activity and progression to inform clinical trial design. For drugs that inhibit the expression of DUX4, measuring DUX4 or DUX4 target gene expression might be an interim outcome measure of drug activity, however, only a subset of muscle biopsies in FSHD show evidence of DUX4 expression.

Read the full summary ↓

Our prior study showed that MRI T2-STIR positive muscles had a higher probability of showing DUX4 expression than muscles with normal MRI characteristics. In the current study, we performed a one-year follow-up assessment of the same muscle with repeat MRI and muscle biopsy. There was very little change in the muscle MRI characteristics over the one-year period and, similar to the initial evaluation MRI T2-STIR-postive muscles had a higher expression of DUX4 regulated genes, as well as genes associated with inflammation, extracellular matrix, and cell cycle. Compared to the initial evaluation, overall the level of expression in these gene categories remained stable over the one-year period, however, there was some variability for each individual muscle biopsied. We pooled the data from both the initial and one-year follow-up evaluations and identified several subgroups based on gene expression, as well as a set of genes that distinguished all of the FSHD samples from the controls that include DUX4-regulated genes, inflammatory immune genes, and cell cycle control genes. These candidate markers of disease activity need to be validated on independent datasets, but will hopefully be useful in studies of disease progression and response to therapy.

This dataset

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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 GSE140261_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 PRJNA589062 and SRA study SRP229610. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 32083293) ↗

Samples in this study

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+ 35 more — browse all 35 samples with per-sample file links →

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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.