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DAXX Directs H3.4-to-H3.3 Histone Replacement During Spermatogenesis [Cut & Run]

GSE308004 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 36 samples Submitted 2026/01/13 Platform GPL34290
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 36 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Mus musculus (mouse)
Samples
36 samples: 18 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
DAXX directs dual modes of H3.4-to-H3.3 histone replacement in the male germlineGenes & development · 2026
Summary (written by the submitters)
During spermatogenesis, extensive chromatin remodeling and histone replacement reshape the male germline epigenome. While HIRA is known to mediate transcription-coupled incorporation of histone variant H3.3, we identify DAXX as a key histone chaperone directing genome-wide, transcription-dependent replacement of H3.4 (H3T) with H3.3 on autosomes during male meiosis.
Read the full summary ↓
Simultaneously, DAXX also directs transcription-independent H3.4-to-H3.3 replacement on the sex chromosomes during meiotic sex chromosome inactivation (MSCI). These distinct, chromosome-specific modes of DAXX-mediated H3.3 deposition are essential for epigenomic integrity in the male germline. Loss of DAXX disrupts this process, leading to widespread transcriptional dysregulation in haploid round spermatids and male infertility.
Published in
DAXX directs dual modes of H3.4-to-H3.3 histone replacement in the male germline
Yeh YH, Hu M, Otsuka K et al. · Genes & development 2026 · PMID 41980770 · doi:10.1101/gad.353435.125
This dataset
Open GSE308004 in finder → Find more mouse ChIP / ATAC / CUT&Tag 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 GSE308004_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1328499 and SRA study SRP620315. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41980770) ↗
Study design
18 conditions, mostly in duplicate
H312_CUTRun_4wk_PS_Daxx_ctrl ×2 H312_CUTRun_4wk_PS_Daxx_cKO ×2 H33_CUTRun_4wk_PS_Daxx_ctrl ×2 H33_CUTRun_4wk_PS_Daxx_cKO ×2 H3t_CUTRun_4wk_PS_Daxx_ctrl ×2 H3t_CUTRun_4wk_PS_Daxx_cKO ×2 H3K9me3_CUTRun_4wk_PS_Daxx_ctrl ×2 H3K9me3_CUTRun_4wk_PS_Daxx_cKO ×2 +10 more

Supports a between-group comparison across 36 samples.

How we read this: 18 replicated groups read from 36 sample titles; they account for 36 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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