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Single-cell RNA-seq Analyses of Oocytes and Zygotes Reveal Earlier Maternal to Zygote Transition in Mice and Rats

GSE287856 Rattus norvegicus (rat) Single-cell RNA-seq 65 samples Submitted 2025/01/23 Platform GPL17021Platform GPL18694
At a glance

Single-cell RNA-seq · rat · 65 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Rattus norvegicus (rat)
Samples
65 samples: 17 × mouse, zygote, single cell sample vs 17 × mouse, MII oocyte, single cell sample vs 16 × rat, zygote, single cell sample vs 15 × rat, MII oocyte, single cell sampleGroups 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.
Summary (written by the submitters)
The maternal to zygote transition in mammals has been an area of intensive research over the past few decades, with an ever-changing landscape of understanding that has accompanied the rapid development of cell-profiling technology. Utilizing a full-length single cell RNA-seq protocol, we profiled mature oocytes and zygotes of mice and rats to uncover elusive transcriptomic dynamics during the maternal to zygote transition.
Read the full summary ↓
We confirm the existence of early gene expression in the mouse zygote while revealing a similar chain of events occurring in the rat zygote. We observe an increase in nascent transcription in both species. Moreover, we find subtle but pervasive signals of differential splicing of genes related to key early zygotic activities occurring in both species. Meanwhile, we find distinct profiles of alternative polyadenylation between zygotes and oocytes in both species, particularly, in genes related to major processes within the zygotes. Finally, although a more dynamic transcriptomic landscape exists in the mouse zygote, the rat zygote also displays similar transcriptomic features, suggesting that minor zygotic activation in rat occurs earlier than originally thought.
This dataset
Open GSE287856 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 GSE287856_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1214818 and SRA study SRP559444. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
17 × mouse, zygote, single cell sample vs 17 × mouse, MII oocyte, single cell sample vs 16 × rat, zygote, single cell sample vs 15 × rat, MII oocyte, single cell sample

Supports a between-group comparison across 65 samples.

How we read this: 4 replicated groups read from 65 sample titles; they account for 65 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

+ 25 more — browse all 65 samples with per-sample file links →

Datasets on a similar topic

Search all 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.