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Inflammatory memory in macrophages emerges from coordinated transcription factor and chromatin dynamics

GSE260996 Mus musculus (mouse) RNA-seq (gene expression) 33 samples Submitted 2025/03/04 Platform GPL21626
At a glance

RNA-seq (gene expression) · mouse · 33 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
33 samples: 11 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
Macrophage memory emerges from coordinated transcription factor and chromatin dynamicsCell systems · 2025
Summary (written by the submitters)
RNA seq for murine bone marrow derived macrophages stimulated with either polyI:C (1000 ng/mL) or CPG (300 nM/mL) for 4 hours followed by TNF (10 ng/mL) or LPS (1 ng/mL) for 4 hours. Controls are 4 hours media followed by polyI:C/CpG/LPS/TNF or polyI:C/CpG followed by media.
Published in
Macrophage memory emerges from coordinated transcription factor and chromatin dynamics
Wang AG, Son M, Gorin A et al. · Cell systems 2025 · PMID 39938520 · doi:10.1016/j.cels.2025.101171
This dataset
Open GSE260996 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 GSE260996_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 PRJNA1084797 and SRA study SRP493666. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39938520) ↗
Study design
11 conditions, mostly in triplicate
CPG_media ×3 CPG_LPS ×3 CPG_TNF ×3 media_CPG ×3 media_media ×3 media_LPS ×3 media_polyIC ×3 media_TNF ×3 +3 more

Supports a between-group comparison across 33 samples.

How we read this: 11 replicated groups read from 33 sample titles; they account for 33 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
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.