GEO series

Single cell sequencing of the effects of blocking lymphotoxin alpha in the mesenteric lymph node and spleen

GSE296503 Mus musculus (mouse) Single-cell RNA-seq 21 samples Submitted 2025/08/01 Platform GPL34290

At a glance

Single-cell RNA-seq · mouse · 21 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 21 samples: 21 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: Distinct roles for B cell-derived LTα3 and LTα1β2 in TNF-mediated ileitisNature immunology · 2025

Summary (written by the submitters)

TNFDARE+/- mice develop TNF-driven transmural ileitis and mesenteric inflammation, and lose body mass, reminiscent of human Crohn’s disease. Here, we report that B cells regulate body mass and intestinal permeability during ileitis in a manner that is linked to lymphotoxin (LT)-a but not LTb, whereas B cell LTab2 promoted mesenteric TLS that suppressed lymphatic outflow.

Read the full summary ↓

Using genetic approaches and neutralizing reagents, we connect LTa3, a ligand for TNFRs, expressed by activated follicular B cells to their appearance in draining lymph nodes and the generation or persistence of IgA+ ileal plasma cells. Some of the same B cells also expressed TNF. Opposite to LTa, expression of TNF by B cells was disadvantageous to the development of IgA+ ileal plasma cells, suggesting counterbalancing interplay between LTa3 and TNF in ileitis. These data highlight a multi-faceted role of B cells in ileitis that includes an unexpected role for B cell-derived LTa3 in the maintenance of body weight.

Published in

Distinct roles for B cell-derived LTα3 and LTα1β2 in TNF-mediated ileitis

Erlich EC, Alayo QA, Kim A et al. · Nature immunology 2025 · PMID 40921841 · doi:10.1038/s41590-025-02263-y

This dataset

Open GSE296503 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 GSE296503_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1259518 and SRA study SRP583407. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40921841) ↗

Study design

21 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 21 sample titles: 21 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

GSM8971796 Mesenteric Lymph Node, WT, Isotype, scRNA-seq
GSM8971797 Mesenteric Lymph Node, WT, Isotype, BCR-seq
GSM8971798 Mesenteric Lymph Node, WT, Isotype, TCR-seq
GSM8971799 Mesenteric Lymph Node, WT, anti-LTa3, scRNA-seq
GSM8971800 Mesenteric Lymph Node, WT, anti-LTa3, BCR-seq
GSM8971801 Mesenteric Lymph Node, WT, anti-LTa3, TCR-seq
GSM8971802 Mesenteric Lymph Node, TNFdARE, Isotype, scRNA-seq
GSM8971803 Mesenteric Lymph Node, TNFdARE, Isotype, BCR-seq
GSM8971804 Mesenteric Lymph Node, TNFdARE, Isotype, TCR-seq
GSM8971805 Mesenteric Lymph Node, TNFdARE, anti-LTa3, scRNA-seq
GSM8971806 Mesenteric Lymph Node, TNFdARE, anti-LTa3, BCR-seq
GSM8971807 Mesenteric Lymph Node, TNFdARE, anti-LTa3, TCR-seq
GSM8971808 Spleen, WT, Isotype, scRNA-seq
GSM8971809 Spleen, WT, Isotype, BCR-seq
GSM8971810 Spleen, WT, Isotype, TCR-seq
GSM8971811 Spleen, TNFdARE, Isotype, scRNA-seq
GSM8971812 Spleen, TNFdARE, Isotype, BCR-seq
GSM8971813 Spleen, TNFdARE, Isotype, TCR-seq
GSM8971814 Spleen, TNFdARE, anti-LTa3, scRNA-seq
GSM8971815 Spleen, TNFdARE, anti-LTa3, BCR-seq
GSM8971816 Spleen, TNFdARE, anti-LTa3, TCR-seq

Datasets on a similar topic

GSE288743 Single-Cell RNA Sequencing of Bone Marrow ILC2p and CHILPs, and Lung and Mesenteric Lymph Node ILC2s 9 samples shares mesenteric, lymph, node
GSE94517 Transcriptomic analysis of reovirus-induced host responses in mesenteric lymph node, lamina propria, peyer's patches, and epithelium. 71 samples shares mesenteric, lymph, node
GSE172279 Bulk RNAseq of Sort-purified IV- Primary (1M) or Quaternary (4M) Tcirc (IV- CD69-/CD103-) or Trm (IV- CD69+/CD103+) Memory P14 cells isolated from Spleen or Mediastinal Lymph Nodes 14 samples shares spleen, lymph, node
GSE58145 Transcriptional profile of Foxp3+ regulatory T cells from colon lamina propria and mesenteric lymph node in steady state mice 6 samples shares mesenteric, lymph, node
GSE243972 Gene expression profile at single cell level of lymphocytes extracted from the mesenteric lymph nodes of TCRMOG animals colonized with either Salmonella expressing MOG or OVA 6 samples shares mesenteric, lymph, node
GSE44322 Gene expression profile analysis of mouse whole spleen following infection by lymphocytic choriomeningitis virus (LCMV), comparing LCMV-Armstrong and LCMV-Clone 13 expression patterns at 0, 5, 9, and 30 days 26 samples shares spleen, lymph
GSE302020 Biological processes in hind paws, dorsal root ganglia and spinal cord of lymphotoxin-beta receptor (LTβR) agonist treated mice 24 samples shares lymphotoxin, lymph
GSE308045 The Peptide Genomic Therapy Increases Antibacterial Immunity and Survival in Sepsis by Reprograming the Gene Orthologs of Human Immunodeficiencies in the Spleen and Lungs 11 samples shares spleen, node

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.