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Cellular spermine targets JAK1 to restrain cytokine-mediated autoimmunity (Mouse)

GSE222887 Mus musculus (mouse) RNA-seq (gene expression) 40 samples Submitted 2024/06/21 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 40 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
40 samples: 8 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
Cellular spermine targets JAK signaling to restrain cytokine-mediated autoimmunityImmunity · 2024
Summary (written by the submitters)
Combining metabolomics analyses with an IFN-stimulated response elements reporter system, we identify spermine as a cellular metabolite brake for JAK1 signaling. Spermine directly binds to FERM and SH2 domains of JAK1 to impair IFNAR2-JAK1 interaction. Spermine suppresses JAK1 phosphorylation triggered by types I and II cytokines, including IFN-I/II, IL-2, and IL-6. Spermine treatment attenuates autoimmune pathogenesis in a SLE murine model and reduces IFN-I signaling in monocytes from SLE patients, which have reduced spermine levels.
Published in
Cellular spermine targets JAK signaling to restrain cytokine-mediated autoimmunity
Xu H, Zhang X, Wang X et al. · Immunity 2024 · PMID 38908373 · doi:10.1016/j.immuni.2024.05.025
This dataset
Open GSE222887 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 GSE222887_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 PRJNA923703 and SRA study SRP417437. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38908373) ↗
Study design
8 conditions, mostly with about 6 replicates each
Ifnar1+/+_PBS_d4 ×6 Ifnar1+/+_PBS_d6 ×6 Ifnar1+/+_spm_d4 ×6 Ifnar1+/+_spm_d6 ×6 Ifnar1-/-_PBS_d4 ×5 Ifnar1-/-_PBS_d6 ×5 Ifnar1+/+_uni ×3 Ifnar1-/-_uni ×3

Supports a between-group comparison across 40 samples.

How we read this: 8 replicated groups read from 40 sample titles; they account for 40 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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