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DAXX governs the silencing of LINE1 during 1 spermatogenesis in mice

GSE293055 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 40 samples Submitted 2025/04/01 Platform GPL24247Platform GPL34290Platform GPL34328
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 40 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
40 samples: 16 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
DAXX governs the silencing of LINE1 during spermatogenesis in miceNucleic acids research · 2026
Summary (written by the submitters)
The disinhibition of transposon elements (TEs) is a significant threat to male reproduction, particularly during the delicate process of spermatogenesis. Here we identify that Death associated protein 6 (Daxx), a potent transcription repressor and an H3.3 chaperone essential for the TEs silencing during spermatogenesis. DAXX-deficient mouse display delayed meiotic progression, reduced production of spermatids, deformed spermatozoa and age-dependent decline in male fertility.
Read the full summary ↓
We demonstrate that young long-interspersed nuclear elements (LINE1) and endogenous retroviral elements (ERVs) subfamilies, were upregulated in meiotic spermatocytes of Daxx null testes. Further study found that the Daxx mutant meiotic cells exhibit DNA hypomethylation in TEs. In summary, we have identified DAXX as a previously unknown key regulator of spermatogenesis that may function as an epigenetic regulator to silence young LINE1 by DNA methylation.
Published in
DAXX governs the silencing of LINE1 during spermatogenesis in mice
Li Z, Xiong C, Shen J et al. · Nucleic acids research 2026 · PMID 41773015 · doi:10.1093/nar/gkag141
This dataset
Open GSE293055 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 GSE293055_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 PRJNA1225444 and SRA study SRP568175. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41773015) ↗
Study design
16 conditions, mostly in triplicate
RNA-seq, meiotic cells, Wild type, biol ×3 RNA-seq, meiotic cells, Daxx knockdown, biol ×3 RNA-seq, round sperm, Wild type, biol ×3 RNA-seq, round sperm, Daxx knockdown, biol ×3 ATAC-seq, meiotic cells, Wild type, biol ×3 ATAC-seq, meiotic cells, Daxx knockdown, biol ×3 ATAC-seq, round sperm, Wild type, biol ×3 ATAC-seq, round sperm, Daxx knockdown, biol ×3 +8 more

Supports a case/control comparison: 20 samples read as cases, 20 as controls.

How we read this: 16 replicated groups read from 40 sample titles; they account for 40 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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