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Epigenetic inheritance of diet-induced and sperm-borne mitochondrial RNAs

GSE239815 Homo sapiens (human) Non-coding RNA profiling 307 samples Submitted 2024/04/03 Platform GPL17021Platform GPL24676Platform GPL24247
At a glance

Non-coding RNA profiling · human · 307 samples

What it is
Non-coding RNA profilingLevels of RNAs that do not code for proteins, such as miRNA or lncRNA.
Organism
Homo sapiens (human)
Samples
307 samples: 21 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
Epigenetic inheritance of diet-induced and sperm-borne mitochondrial RNAsNature · 2024
Summary (written by the submitters)
Spermatozoa harbor a complex and environment sensitive pool of small non-coding RNAs (sncRNA)1, which influences offspring development and adult phenotypes1-7. Whether spermatozoa in the epididymis are directly susceptible to environmental cues is not fully understood8. We used two distinct paradigms of preconception acute high fat diet to dissect epididymal vs testicular contributions to the sperm sncRNA pool and offspring health.
Read the full summary ↓
We show that epididymal spermatozoa, but not developing germ cells, are sensitive to the environment and identify mitochondrial tRNAs and their fragments (mt-tsRNA) as sperm-borne factors. In humans, mt-tsRNAs in spermatozoa correlate with BMI and paternal overweight at conception doubles offspring obesity risk and compromises metabolic health. Sperm sncRNA-seq of mice mutant for genes involved in mitochondrial function, and metabolic phenotyping of their wild-type offspring, suggest that alterations of mt-tsRNAs are downstream of mitochondrial dysfunction. Most importantly, single embryo transcriptomics of genetically hybrid two-cell embryos demonstrated sperm-to-oocyte transfer of mt-tRNAs at fertilisation and implied them in the control of early embryo transcription. Our study supports the importance of paternal health at conception for offspring metabolism, shows that mt-tRNAs are diet-induced and sperm-borne and demonstrates, for the first time in a physiological setting, father-to-offspring transfer of sperm mitochondrial RNAs at fertilization. This SuperSeries is composed of the SubSeries listed below.
Published in
Epigenetic inheritance of diet-induced and sperm-borne mitochondrial RNAs
Tomar A, Gomez-Velazquez M, Gerlini R et al. · Nature 2024 · PMID 38839949 · doi:10.1038/s41586-024-07472-3
This dataset
Open GSE239815 in finder → Find more 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 GSE239815_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 PRJNA1001005 and SRA study SRP452597. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38839949) ↗
Study design
21 conditions, mostly in triplicate
HFD ×122 LoowFD ×99 Human Sperm ×19 Round Spermatids smallrna HFD ×4 Round Spermatids smallrna LFD ×4 Sperm smallrna HFD ×4 Sperm smallrna LFD ×4 Morula LFD ×3 +22 more

Supports a between-group comparison across 298 samples.

How we read this: 21 replicated groups read from 307 sample titles; they account for 298 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

+ 267 more — browse all 307 samples with per-sample file links →

Datasets on a similar topic

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