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Signatures of IL1b, IL6 and TNFa in immune cell-types

GSE239946 Mus musculus (mouse) RNA-seq (gene expression) 209 samples Submitted 2025/01/14 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 209 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
209 samples: 67 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
Early transcriptional effects of inflammatory cytokines reveal highly redundant cytokine networksThe Journal of experimental medicine · 2025
Summary (written by the submitters)
A complete profiling of inflammatory cytokines (IL1b, IL6 and TNFa) in 14 immune cell-types
Published in
Early transcriptional effects of inflammatory cytokines reveal highly redundant cytokine networks
Lee JJ, Yang L, Kotzin JJ et al. · The Journal of experimental medicine 2025 · PMID 39873673 · doi:10.1084/jem.20241207
This dataset
Open GSE239946 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 GSE239946_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 PRJNA1001800 and SRA study SRP453107. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39873673) ↗
Study design
67 conditions, mostly in triplicate
MFpc.PBS.PC ×5 NK.PBS.Sp ×5 Tgd.PBS.Sp ×5 Treg.PBS.Sp ×5 MFrp.PBS.Sp ×5 Mo.6C+.PBS.Sp ×5 GN.PBS.Sp ×5 pDC.PBS.Sp ×5 +59 more

Supports a between-group comparison across 209 samples.

How we read this: 67 replicated groups read from 209 sample titles; they account for 209 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

+ 169 more — browse all 209 samples with per-sample file links →

Datasets on a similar topic

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.