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Marginal zone B cells receive robust Notch2 signals within the B cell follicle in the absense of S1pr1 signaling.

GSE274990 Mus musculus (mouse) RNA-seq (gene expression) 42 samples Submitted 2024/10/18 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 42 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
42 samples: 12 conditions, mostly with about 4 replicates eachGroups 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
Splenic fibroblasts control marginal zone B cell movement and function via two distinct Notch2-dependent regulatory programsImmunity · 2025
Summary (written by the submitters)
Marginal zone (MZ) B cells have innate-like response characteristics due to a unique ability receive and integrate Notch2 signals in the spleen. There is evidence showing MZ B cells receive these signals both in the marginal sinus and the B cell follicle. The relative strength and conservation of these Notch signals is not yet clear. Therefore, we generated mice in which S1pr1 is deleted in mature B cells.
Read the full summary ↓
These mice have MZ B cells by phenotype but these cells are retained in the follicle and unable to transit to the marginal zone. In this experiment we examined the impact of Notch2 signaling in these cells and cre expressing control animals using in vivo anti-Notch2 antibody blockade followed by RNA-sequencing.
Published in
Splenic fibroblasts control marginal zone B cell movement and function via two distinct Notch2-dependent regulatory programs
Allman A, Gaudette BT, Kelly S et al. · Immunity 2025 · PMID 39731910 · doi:10.1016/j.immuni.2024.12.003
This dataset
Open GSE274990 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 GSE274990_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 PRJNA1148923 and SRA study SRP526831. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39731910) ↗
Study design
12 conditions, mostly with about 4 replicates each
control, marginal zone B cell, isotype contro… ×4 S1pr1-/-, marginal zone B cell, isotype contr… ×4 control, marginal zone B cell, anti-Notch2, 4… ×4 control, follicular B cell, isotype control, ×4 S1pr1-/-, follicular B cell, isotype control, ×4 control, follicular B cell, anti-Notch2, 48h, ×4 S1pr1-/-, marginal zone B cell, anti-Notch2, … ×3 control, marginal zone B cell, anti-Notch2, 9… ×3 +4 more

Supports a between-group comparison across 42 samples.

How we read this: 12 replicated groups read from 42 sample titles; they account for 42 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

+ 2 more — browse all 42 samples with per-sample file links →

Datasets on a similar topic

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