GEO series

ILC1 quiescence confers protection against MCMV infections during undernutrition

GSE297741 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2025/12/02 Platform GPL21273

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: Quiescent ILC1 cells confer protection against MCMV infection during undernutritionCell reports · 2025

Summary (written by the submitters)

In the liver, group 1 innate lymphoid cells (ILCs) comprise 10–20% tissue-resident ILC1 cells and 80–90% conventional NK cells. Both cells contribute to early defense against virus infection by secreting IFN-γ. However, the distinct role of ILC1 cells in viral infections remains incompletely understood. Here, we identified that ILC1 cells outnumbered NK cells, constituting 80–90% of group 1 ILCs in the liver during undernutrition.

Read the full summary ↓

Mechanistically, undernutrition significantly reduced NK cell numbers, while hepatic ILC1 cells entered a quiescent state that allowed them to survive in an mTORC1-dependent manner. Metabolically, quiescent ILC1 cells exhibited greater glucose uptake than NK cells and efficiently utilized it via oxidative phosphorylation, which was induced by mTORC1. Finally, ILC1-deficient mice succumbed to MCMV infection under undernourished conditions, but not when fed ad libitum. These findings suggest a non-redundant function of hepatic ILC1 cells in protecting the host against MCMV infection during undernutrition.

Published in

Quiescent ILC1 cells confer protection against MCMV infection during undernutrition

Tatematsu M, Takasuga S, Fuchimukai A et al. · Cell reports 2025 · PMID 41348544 · doi:10.1016/j.celrep.2025.116644

This dataset

Open GSE297741 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 GSE297741_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 PRJNA1266082 and SRA study SRP586983. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41348544) ↗

Study design

8 conditions, mostly in triplicate

WT_NK_AL ×3 WT_NK_C ×3 WT_ILC1_AL ×3 WT_ILC1_C ×3 RaptrCKO_NK_AL ×3 RaptrCKO_NK_C ×3 RaptrCKO_ILC1_AL ×3 RaptrCKO_ILC1_C ×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

GSM8998069 WT_NK_AL_1 WT_NK_AL
GSM8998071 WT_NK_AL_2 WT_NK_AL
GSM8998072 WT_NK_AL_3 WT_NK_AL
GSM8998073 WT_NK_CR_1 WT_NK_C
GSM8998074 WT_NK_CR_2 WT_NK_C
GSM8998075 WT_NK_CR_3 WT_NK_C
GSM8998076 WT_ILC1_AL_1 WT_ILC1_AL
GSM8998077 WT_ILC1_AL_2 WT_ILC1_AL
GSM8998078 WT_ILC1_AL_3 WT_ILC1_AL
GSM8998080 WT_ILC1_CR_1 WT_ILC1_C
GSM8998081 WT_ILC1_CR_2 WT_ILC1_C
GSM8998082 WT_ILC1_CR_3 WT_ILC1_C
GSM8998083 RaptrCKO_NK_AL_1 RaptrCKO_NK_AL
GSM8998084 RaptrCKO_NK_AL_2 RaptrCKO_NK_AL
GSM8998085 RaptrCKO_NK_AL_3 RaptrCKO_NK_AL
GSM8998086 RaptrCKO_NK_CR_1 RaptrCKO_NK_C
GSM8998087 RaptrCKO_NK_CR_2 RaptrCKO_NK_C
GSM8998089 RaptrCKO_NK_CR_3 RaptrCKO_NK_C
GSM8998090 RaptrCKO_ILC1_AL_1 RaptrCKO_ILC1_AL
GSM8998091 RaptrCKO_ILC1_AL_2 RaptrCKO_ILC1_AL
GSM8998092 RaptrCKO_ILC1_AL_3 RaptrCKO_ILC1_AL
GSM8998093 RaptrCKO_ILC1_CR_1 RaptrCKO_ILC1_C
GSM8998094 RaptrCKO_ILC1_CR_2 RaptrCKO_ILC1_C
GSM8998095 RaptrCKO_ILC1_CR_3 RaptrCKO_ILC1_C

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GSE267792 Transcriptional characterization of ILC1 and different subsets of ILC3s lacking REV-ERBs. 30 samples shares ilc1
GSE271252 Transcriptional analysis of ocular tissue from MCMV infected neonatal mice treated with CXCR3 blocking antibody 30 samples shares mcmv
GSE271251 Transcriptional profiling of eyes from MCMV infected neonatal mice during retinal development 24 samples shares mcmv
GSE267984 Transcriptional characterization of ILC1 and different subsets of ILC3s lacking REV-ERBs. [ Bulk RNA-seq] 24 samples shares ilc1
GSE309461 Bulk RNA sequencing of liver NK cells and ILC1s from T-bet WT vs. inducible Ncr1-T-bet Δ/Δ mice 16 samples shares ilc1
GSE198694 NCBR-123: ILC1s and T cells in the Oral Mucosa 9 samples shares ilc1

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.