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Single-embryo and single-blastomere RNA-seq analysis of 2-cell and 4-cell mouse embryos

GSE300864 Mus musculus (mouse) Single-cell RNA-seq 39 samples Submitted 2026/06/01 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 39 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
39 samples: 12 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.
Summary (written by the submitters)
Understanding how the first cell fate decisions arise in the mammalian embryo remains a central question in developmental biology. While lineage segregation becomes morphologically apparent at the 16-cell stage, increasing evidence suggests that molecular asymmetries emerge much earlier. Here, we systematically profile the transcriptome of whole embryo and individual blastomere of mouse embryos at 2-cell and 4-cell stage using SMART-Seq2.
This dataset
Open GSE300864 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 GSE300864_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 PRJNA1282480 and SRA study SRP594759. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
12 conditions, mostly with about 4 replicates each
Whole_2C ×5 Whole_4C ×4 Split_4C-rep2-blastomere ×4 Split_4C-rep3-blastomere ×4 Split_4C-rep4-blastomere ×4 Split_4C-rep6-blastomere ×4 Split_4C-rep7-blastomere ×4 Split_2C-rep1-blastomere ×2 +4 more

Supports a between-group comparison across 39 samples.

How we read this: 12 replicated groups read from 39 sample titles; they account for 39 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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