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Forced Notch2 signaling instructs TLR and BCR responsiveness in B cells [RNA-Seq]

GSE335245 Mus musculus (mouse) RNA-seq (gene expression) 45 samples Submitted 2026/07/08 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 45 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
45 samples: 15 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.
Summary (written by the submitters)
Marginal zone (MZ) B cells optimize protection against blood-borne bacteria by rapidly producing plasma cells in response to Toll-like Receptor (TLR) ligands. Here, we demonstrate that forced Notch2 instructs this responsiveness for Notch2-independent follicular B cells. Upon stimulation with either TLR4 ligand LPS or B cell receptor crosslinking via anti-IgM, access to Notch2 ligands promoted early transcriptional changes to numerous activation programs.
Read the full summary ↓
These changes include augmenting TLR response programs, early and late mitotic pathways, and key cell growth and protein secretion pathways critical for plasma cell differentiation. We conclude that t uniquely robust hyper-responsiveness can be ascribed to any B cell with access to Notch2 ligands.
This dataset
Open GSE335245 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 GSE335245_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 PRJNA1477801 and SRA study SRP709079. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
15 conditions, mostly in triplicate
follicular B cell cultured on OP9-DL1 cells s… ×3 follicular B cell cultured on OP9-DL1 cells s… ×3 follicular B cell cultured on OP9-DL1 cells s… ×3 follicular B cell cultured on OP9-DL1 cells s… ×3 follicular B cell cultured on OP9-DL1 cells s… ×3 follicular B cell cultured on OP9-DL1 cells s… ×3 follicular B cell cultured on OP9-DL1 cells s… ×3 follicular B cell cultured on OP9-DL1 cells u… ×3 +7 more

Supports a between-group comparison across 45 samples.

How we read this: 15 replicated groups read from 45 sample titles; they account for 45 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

+ 5 more — browse all 45 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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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.