GEO series

MRI and gene signatures in facioscapulohumeral dystrophy muscle: implications for clinical trial design and mechanisms of disease progression

GSE242912 Homo sapiens (human) RNA-seq (gene expression) 64 samples Submitted 2024/10/31 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 64 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: 64 samples: 64 samples, each with a distinct title — no replicated groupsGroups 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)

Identifying the aberrant expression of DUX4 in skeletal muscle as the cause of facioscapulohumeral dystrophy (FSHD) has led to rational therapeutic development and clinical trials. Several studies support the use of MRI characteristics and the expression of DUX4-regulated genes in muscle biopsies as biomarkers of FSHD disease activity and progression.

Read the full summary ↓

We performed lower-extremity MRI and muscle biopsies in the mid-portion of the tibialis anterior (TA) muscles bilaterally in FSHD subjects and validated our prior reports of the strong association between MRI characteristics and expression of genes regulated by DUX4 and other gene categories associated with FSHD disease activity. We further show that measurements of normalized fat content in the entire TA muscle strongly predict molecular signatures in the mid-portion of the TA, indicating that regional biopsies can accurately measure progression in the whole muscle and providing a strong basis for inclusion of MRI and molecular biomarkers in clinical trial design. An unanticipated finding was the strong correlations of molecular signatures in the bilateral comparisons, including markers of B-cells and other immune cell populations, suggesting that a systemic immune cell infiltration of skeletal muscle might have a role in disease progression.

This dataset

Open GSE242912 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 GSE242912_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 PRJNA1015276 and SRA study SRP459764. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

64 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 64 sample titles: 64 distinct titles with little repetition. 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

GSM7774730 Muscle biopsy, 01-0019L
GSM7774731 Muscle biopsy, 01-0019R
GSM7774732 Muscle biopsy, 01-0020L
GSM7774733 Muscle biopsy, 01-0020R
GSM7774734 Muscle biopsy, 01-0021L
GSM7774735 Muscle biopsy, 01-0021R
GSM7774736 Muscle biopsy, 01-0022L
GSM7774737 Muscle biopsy, 01-0022R
GSM7774738 Muscle biopsy, 01-0023L
GSM7774739 Muscle biopsy, 01-0023R
GSM7774740 Muscle biopsy, 01-0024L
GSM7774741 Muscle biopsy, 01-0024R
GSM7774742 Muscle biopsy, 01-0025L
GSM7774743 Muscle biopsy, 01-0025R
GSM7774744 Muscle biopsy, 01-0026L
GSM7774745 Muscle biopsy, 01-0026R
GSM7774746 Muscle biopsy, 01-0028L
GSM7774747 Muscle biopsy, 01-0028R
GSM7774748 Muscle biopsy, 01-0029L
GSM7774749 Muscle biopsy, 01-0029R
GSM7774750 Muscle biopsy, 01-0030L
GSM7774751 Muscle biopsy, 01-0030R
GSM7774752 Muscle biopsy, 01-0031L
GSM7774753 Muscle biopsy, 01-0031R
GSM7774754 Muscle biopsy, 13-0001L
GSM7774755 Muscle biopsy, 13-0001R
GSM7774756 Muscle biopsy, 13-0002L
GSM7774757 Muscle biopsy, 13-0002R
GSM7774758 Muscle biopsy, 13-0003L
GSM7774759 Muscle biopsy, 13-0003R
GSM7774760 Muscle biopsy, 13-0004L
GSM7774761 Muscle biopsy, 13-0004R
GSM7774762 Muscle biopsy, 13-0005L
GSM7774763 Muscle biopsy, 13-0005R
GSM7774764 Muscle biopsy, 13-0006L
GSM7774765 Muscle biopsy, 13-0007L
GSM7774766 Muscle biopsy, 13-0007R
GSM7774767 Muscle biopsy, 13-0009L
GSM7774768 Muscle biopsy, 13-0009R
GSM7774769 Muscle biopsy, 13-0010L

+ 24 more — browse all 64 samples with per-sample file links →

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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.