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SLAMF1 is regulated by macrophage-CD4 T cell contact and confers protection to Mycobacterium tuberculosis

GSE224054 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2025/06/18 Platform GPL21103
At a glance

RNA-seq (gene expression) · mouse · 16 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
16 samples: 16 samples, each with a distinct title — no replicated groupsGroups 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
Macrophage-T cell interactions promote SLAMF1 expression for enhanced TB defenseNature communications · 2025
Summary (written by the submitters)
CD4 T cells are crucial for protective immunity to Mycobacterium tuberculosis (Mtb). Because CD4 T cell protection depends upon direct interaction with infected macrophages, we sought to identify contact-dependent protective factors. We discovered that direct contact with antigen-specific CD4 T cells drives signaling lymphocytic activation molecule family member 1 (SLAMF1/CD150) expression on macrophages.
Read the full summary ↓
SLAMF1 is a cell-surface receptor that mediates homotypic interactions between hematopoietic cells, interacts with microbes, and promotes macrophage antimicrobial responses. In mice, SLAMF1 expression was induced on Mtb-infected myeloid cells in a T cell-dependent manner and partially impaired in autophagy-deficient macrophages. In non-human primates, antigen presentation by lung macrophages induced SLAMF1 expression in a manner that correlated with T cell abundance and vaccine protection. Finally, in mice SLAMF1 limited Mtb burden and inflammatory responses during Mtb infection. We conclude that SLAMF1 is a T cell contact-dependent factor in macrophages that contributes to host protection from TB.
Published in
Macrophage-T cell interactions promote SLAMF1 expression for enhanced TB defense
Krishna Prasad GVR, Grigsby SJ, Erkenswick GA et al. · Nature communications 2025 · PMID 40701970 · doi:10.1038/s41467-025-61826-7
This dataset
Open GSE224054 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 GSE224054_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 PRJNA929491 and SRA study SRP420045. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40701970) ↗
Study design
16 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 16 sample titles: 16 distinct titles with little repetition. 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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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.