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HIRA-mediated H3.3 deposition preserves hepatocyte cell identity during non-proliferative liver aging [RNA-Seq 2]

GSE324372 Mus musculus (mouse) RNA-seq (gene expression) 20 samples Submitted 2026/04/02 Platform GPL34475
At a glance

RNA-seq (gene expression) · mouse · 20 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
20 samples: 5 × WT_CRISPR_sgRosa26_female_3weeks vs 5 × WT_CRISPR_sgHIRA_female_3weeks vs 5 × WT_CRISPR_sgRosa26_female_6months vs 5 × WT_CRISPR_sgHIRA_female_6monthsGroups 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
HIRA-mediated H3.3 deposition preserves hepatocyte cell identity during liver agingResearch square · 2026
Summary (written by the submitters)
Age-associated functional decline is partly driven by progressive chromatin degeneration. Conversely, maintenance of chromatin integrity preserves cell identity and promotes healthy aging, albeit through different mechanisms in proliferating and non-proliferating cells. However, whether tissue regeneration with its associated cell proliferation can rescue defects in epigenetic maintenance in otherwise non-proliferative cells remains unclear.
Read the full summary ↓
The histone chaperone HIRA deposits the histone variant H3.3 in a DNA replication–independent manner, leading to its accumulation in aging, non-proliferating cells. Here, we show that hepatocyte-specific loss of HIRA causes loss of cell identity, metabolic dysfunction, and accelerated fibrotic pathology with age. Transcriptomic and epigenomic analyses indicate that HIRA–H3.3 preserves chromatin integrity and sustains transcription of highly expressed genes. Partial hepatectomy, associated with induced proliferation, restores cell identity with compensatory deposition of canonical histones H3.1/2. Together, these results demonstrate that HIRA-mediated H3.3 deposition is essential for safeguarding cell identity and tissue function during aging of non-proliferating cells, but this function can be rescued by tissue regeneration with associated cell proliferation.
Published in
HIRA-mediated H3.3 deposition preserves hepatocyte cell identity during liver aging
Adams P, Arnold R, Teneche M et al. · Research square 2026 · PMID 42282022 · doi:10.21203/rs.3.rs-9261217/v1
This dataset
Open GSE324372 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 GSE324372_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 PRJNA1434510 and SRA study SRP682373. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42282022) ↗
Study design
5 × WT_CRISPR_sgRosa26_female_3weeks vs 5 × WT_CRISPR_sgHIRA_female_3weeks vs 5 × WT_CRISPR_sgRosa26_female_6months vs 5 × WT_CRISPR_sgHIRA_female_6months

Supports a between-group comparison across 20 samples.

How we read this: 4 replicated groups read from 20 sample titles; they account for 20 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
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