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Histone H3.3 ensures cell proliferation and genomic stability during myeloid cell development [RNA-seq]

GSE285141 Mus musculus (mouse) RNA-seq (gene expression) 81 samples Submitted 2024/12/30 Platform GPL13112Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 81 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
81 samples: 24 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
Histone H3.3 ensures cell proliferation and genomic stability during myeloid cell developmentiScience · 2026
Summary (written by the submitters)
Variant histone H3.3 is thought to be critical for survival of many cells, since it is deposited in expressed genes, a feature different from core histones. For example, H3.3 deletion leads to embryonic lethality in mice. However, requirement of H3.3 in later stage of development has remained unclear. The aim of this work was to elucidate the role of H3.3 for development of myeloid lineage, important for innate immunity.
Read the full summary ↓
We conditionally knocked out (cKO) the H3.3 genes in myeloid progenitor cells differentiating into bone marrow derived macrophages (BMDMs). Progenitor cells lacking H3.3 were defective in replication, suffered from extensive DNA damage, and underwent apoptosis. Surviving H3.3cKO cells expressed many interferon stimulated genes (ISGs) throughout differentiation. Further, H3.3cKO BMDMs possessed chromatin accessible sites, and histone posttranslational modifications consistent with the gene expression profiles, Accordingly, H3.3cKO BMDMs retained general nucleosomal structure genome wide. In summary, H3.3 is required for proliferation of myeloid progenitor cells, but is in large part dispensable for differentiation of BMDMs.
Published in
Histone H3.3 ensures cell proliferation and genomic stability during myeloid cell development
Chauhan S, Kudoh F, Dey A et al. · iScience 2026 · PMID 42389591 · doi:10.1016/j.isci.2026.116501
This dataset
Open GSE285141 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 GSE285141_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 PRJNA1201234 and SRA study SRP553074. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42389591) ↗
Study design
24 conditions, mostly in triplicate
BMDMs, WT, biol ×6 BMDMs, cKO, biol ×6 BMDM progeniors, WT, day3, biol ×3 BMDM progeniors, cKO, day3, biol ×3 BMDM progeniors, cKO, day5, biol ×3 Peritoneal macrophaes, WT, biol ×3 Peritoneal macrophaes, cKO, biol ×3 BMDMs, WT, no antibody, biol ×3 +25 more

Supports a between-group comparison across 72 samples.

How we read this: 24 replicated groups read from 81 sample titles; they account for 72 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

+ 41 more — browse all 81 samples with per-sample file links →

Datasets on a similar topic

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