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RNA-seq analysis of B cells cultured with LPS and IL-12 and/or IFN gamma

GSE231931 Mus musculus (mouse) RNA-seq (gene expression) 42 samples Submitted 2024/05/15 Platform GPL30172
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: 14 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
IL-12 induces a B cell-intrinsic IL-12/IFNγ feed-forward loop promoting extrafollicular B cell responsesNature immunology · 2024
Summary (written by the submitters)
Purpose: We aimed to find genes differentially regulated by IL-12 and IFNg alone, and in combination, over 4 and 24 hours of stimulation. Methods : Spleens were processed and B cell cultures prepared, in triplicate, according to the manuscript. After the indicated times, cells were washed in PBS, resuspended in 350 ul RLT Plus Buffer (Qiagen) with 1% 2-Me, and frozen at -80 ⁰C.
Read the full summary ↓
Results: At 4 hours, the main effect of IL-12 is to induce IFNg production from B cells, whereas IFNg induces many gene changes. Comparing 24 hours to the 4 hour stimulation, IFNg alone was insufficient to maintain the majority of IFNg-induced 4 hour changes, while adding IL-12 sustained a portion of the 4 hour gene changes. Additionally, in combination IL-12 and IFNg cooperate to induce unique gene changes that are not shared with either the individual cytokines at either timepoint.
Published in
IL-12 induces a B cell-intrinsic IL-12/IFNγ feed-forward loop promoting extrafollicular B cell responses
Elsner RA, Smita S, Shlomchik MJ · Nature immunology 2024 · PMID 38862796 · doi:10.1038/s41590-024-01858-1
This dataset
Open GSE231931 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 GSE231931_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 PRJNA970259 and SRA study SRP436473. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38862796) ↗
Study design
14 conditions, mostly in triplicate
4 hours, IL-12 at 2000 pg/mL, IFNg block, mou… ×3 4 hours, IL-12 at 2000 pg/mL, IFNg at 0.5 ng/… ×3 4 hours, IL-12 at 200 pg/mL, IFNg at 0.5 ng/m… ×3 4 hours, IL-12 at 200 pg/mL, IFNg block, mouse ×3 4 hours, IL-12 at 20 pg/mL, IFNg at 0.5 ng/mL… ×3 4 hours, IL-12 at 20 pg/mL, IFNg block, mouse ×3 24 hours, IL-12 at 20 pg/mL, IFNg at 0.5 ng/m… ×3 24 hours, IL-12 at 20 pg/mL, IFNg block, mouse ×3 +6 more

Supports a between-group comparison across 42 samples.

How we read this: 14 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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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.