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Epididymal acquired sperm microRNAs modify post-fertilization embryonic gene expression

GSE244885 Mus musculus (mouse) Non-coding RNA profiling 425 samples Submitted 2024/08/31 Platform GPL32159
At a glance

Non-coding RNA profiling · mouse · 425 samples

What it is
Non-coding RNA profilingLevels of RNAs that do not code for proteins, such as miRNA or lncRNA.
Organism
Mus musculus (mouse)
Samples
425 samples: 57 conditions, mostly with about 4 replicates eachGroups 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 acquired sperm microRNAs modify post-fertilization embryonic gene expressionCell reports · 2024
Summary (written by the submitters)
Sperm small RNAs have emerged as important non-genetic contributors to embryogenesis and offspring health. A subset of sperm small RNAs are thought to be acquired during epididymal transit. However, the transfer of RNAs from the somatic epididymis to the sperm has been questioned, and the identity of the specific small RNAs transferred remains unclear.
Read the full summary ↓
Here, we employ Cre/Lox genetics to generate germline- and epididymal-specific Dgcr8 conditional knockout mice to investigate the dynamics of sperm microRNAs and their function in the early embryo. Interestingly, sperm from germline specific Dgcr8 knockout males restored the levels of 58 of the 98 (59%) miRNAs that were lost in testicular sperm during epididymal transit. Conversely, sperm from epididymal Dgcr8 knockouts displayed a 5-fold reduction in 25 miRNAs. This substantial loss of epididymal miRNAs in sperm was accompanied by transcriptomic changes in the embryo which was rescued by microinjection of epididymal miRNAs. These findings ultimately demonstrate the acquisition of miRNAs by sperm during epididymal transit and their regulation of post-fertilization embryonic gene expression.
Published in
Epididymal acquired sperm microRNAs modify post-fertilization embryonic gene expression
Trigg NA, Conine CC · Cell reports 2024 · PMID 39226174 · doi:10.1016/j.celrep.2024.114698
This dataset
Open GSE244885 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 GSE244885_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 ↗

Also filed as BioProject PRJNA1025273 and SRA study SRP465035. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39226174) ↗
Study design
57 conditions, mostly with about 4 replicates each
s8_tssp_M_het ×27 s8_tssp_4_het ×22 s8_tssp_4_homo ×22 s8_tssp_M_homo ×21 s8_causp_4_het ×18 s8_causp_4_dg ×15 defb_het_causp ×8 defb_homo_causp ×8 +49 more

Supports a between-group comparison across 400 samples.

How we read this: 57 replicated groups read from the first 400 of 425 sample titles; they account for 400 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

+ 385 more — browse all 425 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.