GEO series

Fidelity in lineage determination and stimulus-inducible gene expression requires ISWI chromatin remodeling activity [RNA-Seq 2]

GSE297169 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2025/09/18 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 16 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: 16 samples: 8 conditions, mostly in duplicateGroups 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: Control of myeloid lineage fidelity and response to stimuli by ISWI-enforced nucleosome phasingImmunity · 2025

Summary (written by the submitters)

Control over the accessibility of the genomic cis-regulatory information is key for the accurate deployment of gene expression programs. Such control is exerted by the combined action of pioneer transcription factors and chromatin remodelers with different ability to alter nucleosome positioning and occupancy. Here we show that SMARCA5 ( SNF2H), a chromatin remodeler enforcing linker DNA length, controls spacing of nucleosomes adjacent to sites where the myeloid lineage determining and pioneer TF PU.1 is constitutively bound, without however affecting PU.1 binding.

Read the full summary ↓

Loss of SMARCA5 caused a widespread increase in the accessibility of sites for stimulus-regulated TFs, causing not only macrophage hyper-activation in response to inflammatory stimulation but also the induction of stimulus-inappropriate genes. SMARCA5 deficiency also determined the extensive increase in binding of C/EBPb to cognate sites normally not accessible in macrophages but instead exposed in white or brown adipogenesis. Overall, enforcement of nucleosome phasing by ISWI controls fidelity in both lineage specification and response to stimulation.

Published in

Control of myeloid lineage fidelity and response to stimuli by ISWI-enforced nucleosome phasing

Polletti S, Melià-Alomà J, Pileri F et al. · Immunity 2025 · PMID 41005292 · doi:10.1016/j.immuni.2025.09.002

This dataset

Open GSE297169 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 GSE297169_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 PRJNA1262916 and SRA study SRP585352. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41005292) ↗

Study design

8 conditions, mostly in duplicate

SMARCA5 KOBMDM, 1h MRT67307 (5 µM), 2h LPS 10… ×2 SMARCA5 KOBMDM, 1h MRT67307 (5 µM), ×2 SMARCA5 KOBMDM, 2h LPS 10ng/ml, ×2 SMARCA5 KOBMDM, untreated, ×2 WT BMDM, 1h MRT67307 (5 µM), 2h LPS 10ng/ml, ×2 WT BMDM, 1h MRT67307 (5 µM), ×2 WT BMDM, 2h LPS 10ng/ml, ×2 WT BMDM, untreated, ×2

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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

GSM8984907 SMARCA5 KOBMDM, 1h MRT67307 (5 µM), 2h LPS 10ng/ml, replicate1 SMARCA5 KOBMDM, 1h MRT6…
GSM8984908 SMARCA5 KOBMDM, 1h MRT67307 (5 µM), 2h LPS 10ng/ml, replicate2 SMARCA5 KOBMDM, 1h MRT6…
GSM8984909 SMARCA5 KOBMDM, 1h MRT67307 (5 µM), replicate1 SMARCA5 KOBMDM, 1h MRT6…
GSM8984910 SMARCA5 KOBMDM, 1h MRT67307 (5 µM), replicate2 SMARCA5 KOBMDM, 1h MRT6…
GSM8984911 SMARCA5 KOBMDM, 2h LPS 10ng/ml, replicate1 SMARCA5 KOBMDM, 2h LPS …
GSM8984912 SMARCA5 KOBMDM, 2h LPS 10ng/ml, replicate2 SMARCA5 KOBMDM, 2h LPS …
GSM8984913 SMARCA5 KOBMDM, untreated, replicate1 SMARCA5 KOBMDM, untreat…
GSM8984914 SMARCA5 KOBMDM, untreated, replicate2 SMARCA5 KOBMDM, untreat…
GSM8984915 WT BMDM, 1h MRT67307 (5 µM), 2h LPS 10ng/ml, replicate1 WT BMDM, 1h MRT67307 (5…
GSM8984916 WT BMDM, 1h MRT67307 (5 µM), 2h LPS 10ng/ml, replicate2 WT BMDM, 1h MRT67307 (5…
GSM8984917 WT BMDM, 1h MRT67307 (5 µM), replicate1 WT BMDM, 1h MRT67307 (5…
GSM8984918 WT BMDM, 1h MRT67307 (5 µM), replicate2 WT BMDM, 1h MRT67307 (5…
GSM8984919 WT BMDM, 2h LPS 10ng/ml, replicate1 WT BMDM, 2h LPS 10ng/ml,
GSM8984920 WT BMDM, 2h LPS 10ng/ml, replicate2 WT BMDM, 2h LPS 10ng/ml,
GSM8984921 WT BMDM, untreated, replicate1 WT BMDM, untreated,
GSM8984922 WT BMDM, untreated, replicate2 WT BMDM, untreated,

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