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The intestinal microbiota modulates the transcriptional landscapes of iNKT cells

GSE242752 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2024/03/14 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 24 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
24 samples: 8 conditions, mostly in triplicateGroups 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
The intestinal microbiota modulates the transcriptional landscape of iNKT cells at steady-state and following antigen exposureMucosal immunology · 2024
Summary (written by the submitters)
Invariant Natural Killer T (iNKT) cells are unconventional T cells that respond to microbe-derived glycolipid antigens. iNKT cells exert fast innate effector functions that regulate immune responses in a variety of contexts, including during infection, cancer, or inflammation. The roles these unconventional T cells play in intestinal inflammation remain poorly defined and vary based on the disease model and species.
Read the full summary ↓
Our previous work suggested that the gut microbiota influenced iNKT cell functions during dextran sulfate sodium-induced colitis in mice. This study, shows that iNKT cell homeostasis and response following activation are altered in germ-free mice. Using prenatal fecal transplant in specific pathogen-free mice, we show that the transcriptional signatures of iNKT cells at steady state and following αGC-mediated activation in vivo are modulated by the microbiota. Our data suggest that iNKT cells sense the microbiota at homeostasis independently of their T cell receptors. Finally, iNKT cell transcriptional signatures are different in male and female mice. Collectively, our findings suggest that sex and the intestinal microbiota are important factors that regulate iNKT cell homeostasis and responses. A deeper understanding of microbiota-iNKT cell interactions and the impact of sex could improve the development of iNKT cell-based immunotherapies.
Published in
The intestinal microbiota modulates the transcriptional landscape of iNKT cells at steady-state and following antigen exposure
Lin Q, Kuypers M, Baglaenko Y et al. · Mucosal immunology 2024 · PMID 38331095 · doi:10.1016/j.mucimm.2024.02.002
This dataset
Open GSE242752 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 GSE242752_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 PRJNA1014458 and SRA study SRP459361. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38331095) ↗
Study design
8 conditions, mostly in triplicate
mLN iNKT cells, PBS, female, WT FT, ×3 mLN iNKT cells, PBS, male, WT FT, ×3 mLN iNKT cells, aGC, female, WT FT, ×3 mLN iNKT cells, aGC, male, WT FT, ×3 mLN iNKT cells, PBS, female, KO FT, ×3 mLN iNKT cells, PBS, male, KO FT, ×3 mLN iNKT cells, aGC, female, KO FT, ×3 mLN iNKT cells, aGC, male, KO FT, ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 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
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