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A sperm-enriched 5’fragment of tRNA-Valine regulates preimplantation embryonic transcriptome and development

GSE281829 Mus musculus (mouse) RNA-seq (gene expression) 32 samples Submitted 2025/09/30 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 32 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
32 samples: 16 × mmem_val_sl vs 16 × mmem_ctl_slGroups 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
Epididymal dynamics and preimplantation roles of a sperm-enriched 5' fragment of tRNA-valineCell reports · 2025
Summary (written by the submitters)
Sperm small RNAs have been implicated in intergenerational epigenetic inheritance of paternal environmental effects; however, their biogenesis and functions remain poorly understood. We previously identified a 5’ fragment of tRNA-Valine-CAC-2 (tRFValCAC) as one of the most abundant tRNA fragments in mature mouse sperm. We previously reported that tRFValCAC is specifically enriched in sperm during post-testicular maturation in the epididymis, and extracellular vesicles secreted by the epididymis epithelial cells can deliver tRFValCAC to sperm.
Read the full summary ↓
Here, we investigated the mechanistic basis of tRFValCAC delivery from epididymis to sperm and its functions during early embryonic development. We show that tRFValCAC interacts with an RNA binding protein, heterogeneous nuclear ribonucleoprotein A/B (hnRNPAB), in the epididymis and that hnRNPAB regulates the levels of tRFValCAC in the vesicles secreted by epididymis epithelial cells. Inhibition of tRFValCAC in preimplantation embryos altered the transcript abundance of genes involved in RNA splicing and mRNA processing. Importantly, tRFValCAC-inhibited embryos showed altered mRNA splicing, including alternative splicing of various splicing factors and genes important for proper preimplantation embryonic development. Moreover, our data suggest that tRFValCAC regulates its target genes via interaction with RNA-binding proteins. Finally, we find that inhibition of tRFValCAC in zygotes delayed preimplantation embryonic development. Together, our results reveal a potential function of a sperm-enriched tRF in regulating alternating splicing and preimplantation embryonic development and shed light on the mechanism of sperm small RNA-mediated epigenetic inheritance.
Published in
Epididymal dynamics and preimplantation roles of a sperm-enriched 5' fragment of tRNA-valine
Liu S, Holmes AD, Gupta A et al. · Cell reports 2025 · PMID 41042673 · doi:10.1016/j.celrep.2025.116366
This dataset
Open GSE281829 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 GSE281829_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 PRJNA1185779 and SRA study SRP545070. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41042673) ↗
Study design
16 × mmem_val_sl vs 16 × mmem_ctl_sl

Supports a between-group comparison across 32 samples.

How we read this: 2 replicated groups read from 32 sample titles; they account for 32 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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