GEO series

RNA m6A methylome in mouse oocytes and preimplantation embryos

GSE192440 Mus musculus (mouse) DNA methylation 24 samples Submitted 2023/02/10 Platform GPL24247

At a glance

DNA methylation · mouse · 24 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Mus musculus (mouse)
Samples: 24 samples
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.

Summary (written by the submitters)

N6-methyladenosine (m6A), the most prevalent internal modification in eukaryotic messenger RNA, plays diverse regulatory roles in many biological processes and is involved in a variety of physiological behaviors. Here we present the m6A methylome maps of mouse oocytes and preimplantation embryos by a low-input approach picoMeRIP-seq. We revealed that m6A was largely and dynamically deposited on maternal and zygotic RNAs during maternal-to-zygotic transition (MZT), especially on those encoding the factors essential for cell fate determination.

Read the full summary ↓

m6A frequently marked the maternally-derived RNAs to be degraded and the genes that were activated during zygotic genome activation. Moreover, the RNAs derived from retrotransposons, such as MTA and MERVL, were heavily occupied by m6A. Collectively, our results provide a foundation for future studies exploring the regulatory roles of m6A in mammalian early embryo development.

This dataset

Open GSE192440 in finder → Find more mouse methylation 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 GSE192440_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 beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA791403 and SRA study SRP352000. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37081317) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 24 more — browse all 24 samples with per-sample file links →

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GSE316549 Loss of maternal PADI6 disrupts DNA methylation and genomic imprinting maintenance in late preimplantation mouse embryos. 19 samples shares preimplantation, embryos
GSE282209 Single-nucleus chromatin accessibility landscape in mouse preimplantation embryos 12 samples shares preimplantation, embryos
GSE234968 Preventing CpG hypermethylation in oocytes safeguards mouse development 612 samples shares oocytes

Search all mouse methylation 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.