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Distinct roles of the corepressors NCOR and SMRT in shaping the macrophage epigenome and transcriptome linked to metabolic and inflammatory pathways

GSE291538 Mus musculus (mouse) RNA-seq (gene expression) 21 samples Submitted 2025/09/24 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 21 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
21 samples: 7 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
SMRT anchors the HDAC3 corepressor complex to chromatin to regulate inflammatory and metabolic pathways in macrophagesNucleic acids research · 2025
Summary (written by the submitters)
The NCOR/SMRT corepressor complex is a fundamental coregulator of these mechanisms. However, the individual roles and the relative importance of the two major subunits NCOR and SMRT remain poorly understood. Here, we assessed the genome-wide roles of NCOR and SMRT in mouse macrophages by integrative analysis of cistrome, epigenome, and transcriptome.
Read the full summary ↓
Although both corepressors exhibit genome-wide cooccupancy, their depletion revealed that SMRT primarily represses inflammation-related genes, whereas NCOR primarily represses metabolism-related genes. NCOR also activates inflammatory genes, some characteristic of tumor-associated macrophages. Corepressor depletion selectively alters chromatin accessibility, acetylation at enhancers, and the interplay with transcription factors. Both corepressors influence each other at chromatin, with SMRT superior to NCOR.
Published in
SMRT anchors the HDAC3 corepressor complex to chromatin to regulate inflammatory and metabolic pathways in macrophages
Efthymiadou A, Gu C, Wang C et al. · Nucleic acids research 2025 · PMID 40966497 · doi:10.1093/nar/gkaf880
This dataset
Open GSE291538 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 GSE291538_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 PRJNA1234104 and SRA study SRP569147. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40966497) ↗
Study design
7 conditions, mostly in triplicate
RAW_siCtrl ×3 RAW_siNCO ×3 RAW_siSMRT ×3 BMDM_shGFP_n ×3 BMDM_shGFP_s ×3 BMDM_shNCO ×3 BMDM_shSMRT ×3

Supports a between-group comparison across 21 samples.

How we read this: 7 replicated groups read from 21 sample titles; they account for 21 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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