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Regulation of mRNA polyadenylation governs body plan formation in gastruloids

GSE302657 Mus musculus (mouse) Single-cell RNA-seq 60 samples Submitted 2026/07/13 Platform GPL24247Platform GPL24973Platform GPL34290Platform GPL34328
At a glance

Single-cell RNA-seq · mouse · 60 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
60 samples: 13 conditions, mostly in duplicateGroups 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)
Gastrulation marks a landmark event in early embryogenesis, laying the foundation for the three germ layers and body plan formation. While transcriptional and epigenetic regulation during gastrulation has been extensively studied, post-transcriptional mechanisms remain underexplored, partly due to technical constraints and limited access to mammalian embryos.
Read the full summary ↓
Here, we combine the scalability of gastruloids, an in vivo model of early embryonic development, with a single-cell CRISPR screening platform to systematically dissect post-transcriptional regulators of germ layer differentiation. Our screen uncovers previously unrecognized regulators of mesodermal and endodermal fate and enables cell-type-specific functional characterization with single-cell transcriptomic readout. Focusing on the de-adenylase Cnot8, we demonstrate that Cnot8-mediated poly(A) tail regulation is essential for mesodermal differentiation and proper body axis formation, underscoring the critical role of post-transcriptional control in early mammalian development. Together, our findings support a critical role of poly(A) tail regulation in the patterning of the mammalian embryo and establish gastruloid based single cell CRISPR screens as tool to uncover novel regulators and mechanisms of embryogenesis.
This dataset
Open GSE302657 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 GSE302657_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 PRJNA1291681 and SRA study SRP600939. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
13 conditions, mostly in duplicate
RNA_deg_C8c2_Act ×3 RNA_deg_C8c4_Act ×3 RNA_deg_Ctrl2_Act ×3 RNA_deg_Ctrl11_Act ×3 Gast_124_C7_RNA ×2 Gast_37_48h_96h_Ribo ×2 Gast_37_72h_120h_Ribo ×2 WTA_2 ×2 +35 more

Supports a between-group comparison across 30 samples.

How we read this: 13 replicated groups read from 60 sample titles; they account for 30 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

+ 20 more — browse all 60 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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