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Magnesium supplementation modifies synovial and splenic transcriptomic signatures and biologic pathways in arthritis mice

GSE276773 Mus musculus (mouse) RNA-seq (gene expression) 26 samples Submitted 2024/11/21 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 26 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
Mus musculus (mouse)
Samples
26 samples: 5 conditions, mostly with about 6 replicates eachGroups 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
Magnesium Supplementation Modifies Arthritis Synovial and Splenic Transcriptomic Signatures Including Ferroptosis and Cell Senescence Biological PathwaysNutrients · 2024
Summary (written by the submitters)
Rheumatoid arthritis (RA) is a common chronic autoimmune and inflammatory disease that can cause joint pain and disability. We have recently reported that oral magnesium supplementation significantly reduces disease severity and joint damage in two models of RA. In the synovial tissues.
Read the full summary ↓
There was an enrichment for differentially expressed genes (DEGs) belonging to pathways implicated in transcription regulation, nuclear receptor signaling, and pathways implicated in RA pathogenesis such as RHO GTPases, RUNX1 pathway, oxidative stress induced senescence, senescence-associated secretory phenotype (SASP) and cell migration in synovial tissues . In the synovial tissues Actc1 and Nr4a3 were among the genes with the highest expression, while Krt79 and Ffar2 were among the genes with the most significantly decreased expression in Mg2800 group compared with Mg500. Spleens had an enrichment for Metabolism of folate and pterines, HSP90 chaperone cycle for steroid hormone receptor. Syt5 and Hspa1a were among the genes with the highest expression, while Ano2 and Ascl4 were among the genes with the lowest expression levels in spleens from Mg2800 compared with Mg500. We describe the tissue transcriptomic consequences of the arthritis-protecting increased Mg dietary intake in KSIA mice. These results show that oral Mg supplementation may interfere with pathways implicated response to oxidative stress and senescence, and other processes known to participate in RA pathogenesis. Our findings provide new evidence supporting the disease-suppressing effect of increased Mg intake in arthritis. Oral Mg supplementation has the potential to become a new addition to the therapeutic options for RA and other autoimmune and inflammatory diseases.
Published in
Magnesium Supplementation Modifies Arthritis Synovial and Splenic Transcriptomic Signatures Including Ferroptosis and Cell Senescence Biological Pathways
Laragione T, Harris C, Gulko PS · Nutrients 2024 · PMID 39683640 · doi:10.3390/nu16234247
This dataset
Open GSE276773 in finder → Find more mouse 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 GSE276773_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 PRJNA1158834 and SRA study SRP531657. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39683640) ↗
Study design
5 conditions, mostly with about 6 replicates each
SP-Mg2800 ×7 SY-Mg500 ×6 SY-Mg2800 ×6 SP-Mg500 ×4 SP-Mgg500 ×3

Supports a between-group comparison across 26 samples.

How we read this: 5 replicated groups read from 26 sample titles; they account for 26 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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