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Functional dissection of metabolic trait-associated variants in steady state and stimulated human skeletal muscle cells [RNA-Seq]

GSE282850 Homo sapiens (human) RNA-seq (gene expression) 15 samples Submitted 2025/01/02 Platform GPL34281
At a glance

RNA-seq (gene expression) · human · 15 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
15 samples: 4 × LHCN-M2 cells, undiff, mRNA vs 4 × LHCN-M2 cells, diff, mRNA vs 4 × LHCN-M2 cells, palmitate, mRNA vs 3 × LHCN-M2 cells, AICAR, mRNAGroups 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
Functional dissection of metabolic trait-associated gene regulation in steady state and stimulated human skeletal muscle cellsbioRxiv : the preprint server for biology · 2025
Summary (written by the submitters)
Type 2 diabetes (T2D) is a common metabolic disorder characterized by dysregulation of glucose metabolism. Genome-wide association studies have defined hundreds of signals associated with T2D and related metabolic traits, most of which are found in noncoding regions. Given their central role in insulin production and glucose homeostasis, much focus has been devoted to investigating T2D-associated genetic variation in pancreatic islets; however, metabolic disease pathogenesis and risk is distributed across other important metabolic tissues, including the liver, adipose, and skeletal muscle.
Read the full summary ↓
Here, we performed RNA-seq in human skeletal muscle cells in one of four conditions: (1) undifferentiated or differentiated with (2) basal media, (3) media supplemented with the AMP analog 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) to mimic physiological effects of exercise or (4) media containing sodium palmitate which is known to induce insulin resistance. We used these profiles to identify how relevant metabolic stimuli influence transcriptome-wide gene regulation.
Published in
Functional dissection of metabolic trait-associated gene regulation in steady state and stimulated human skeletal muscle cells
Nishino K, Kitzman JO, Parker SCJ et al. · bioRxiv : the preprint server for biology 2025 · PMID 39677760 · doi:10.1101/2024.11.28.625886
This dataset
Open GSE282850 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 GSE282850_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 PRJNA1169361 and SRA study SRP537592. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39677760) ↗
Study design
4 × LHCN-M2 cells, undiff, mRNA vs 4 × LHCN-M2 cells, diff, mRNA vs 4 × LHCN-M2 cells, palmitate, mRNA vs 3 × LHCN-M2 cells, AICAR, mRNA

Supports a between-group comparison across 15 samples.

How we read this: 4 replicated groups read from 15 sample titles; they account for 15 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
Datasets on a similar topic

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