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Immunoresponsive Gene 1 Facilitates TLR4-agonist-Induced Augmentation of Innate Antimicrobial Immunity

GSE278668 Mus musculus (mouse) RNA-seq (gene expression) 26 samples Submitted 2024/10/09 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: 12 conditions, mostly in duplicateGroups 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)
Treatment with the toll-like receptor (TLR) 4 agonist monophosphoryl lipid A (MPLA) conditions innate immunocytes to respond robustly to subsequent infection, a phenotype termed innate immune memory. Our published studies show that metabolic reprogramming of macrophages is a prominent feature of the memory phenotype. We undertook studies to define the functional contributions of tricarboxylic acid (TCA) reprogramming to innate immune memory.
Read the full summary ↓
We observed that MPLA potently induced expression of immunoresponsive gene 1 (Irg1) and accumulation of its byproduct, the TCA cycle metabolite itaconate, in macrophages. Treatment with MPLA enhanced microbial clearance in wild type (WT), but not Irg1-deficient, mice, demonstrating that itaconate contributes to the antimicrobial phenotype in vivo. Treatment with MPLA equally augmented innate leukocyte recruitment, phagocytosis, respiratory burst and cytokine responses in WT and Irg1-deficient innate leukocytes after infection. However, the ability of Irg1-deficient macrophages to kill Pseudomonas aeruginosa was impaired. We further observed that itaconate is directly antimicrobial against P. aeruginosa at pH 5, which is characteristic of the phagolysosome, and is facilitated by reactive oxygen species. RNA sequencing revealed suppressed transcription of genes associated with phagolysosome function in Irg1 deficient macrophages. This study identifies a contribution of itaconate to MPLA-induced augmentation of innate antimicrobial immunity via facilitation of microbial killing.
This dataset
Open GSE278668 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 GSE278668_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 PRJNA1168170 and SRA study SRP536305. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
12 conditions, mostly in duplicate
Irg1KO BMDM, MPLA, 24h, biol ×2 Irg1KO BMDM, MPLA, 4h, biol ×2 Irg1KO BMDM,DMSO control, biol ×2 Irg1KO BMDM,MPLA, 3dp, biol ×2 Irg1KO BMDM,MPLA then LPS, biol ×2 Irg1KO BMDM, DMSO control, biol ×2 Irg1KO BMDM, LPS, 4hr, biol ×2 WT BMDM, MPLA, 24h, biol ×2 +6 more

Supports a between-group comparison across 24 samples.

How we read this: 12 replicated groups read from 26 sample titles; they account for 24 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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