GEO series

Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution [Smart-seq3-RNA-seq-add]

GSE277789 Mus musculus (mouse) Single-cell RNA-seq 830 samples Submitted 2025/01/16 Platform GPL30215

At a glance

Single-cell RNA-seq · mouse · 830 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 830 samples: 830 samples, each with a distinct title — no replicated groupsGroups 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: Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolutionCell · 2025

Summary (written by the submitters)

During early mammalian development, the endoderm layer undergoes complex patterning to form the foundations of the respiratory and digestive systems. This intricate process, guided by a series of cell fate decisions, remains only partially understood. Our research introduces a pioneering genetic tracing code across 14 distinct endodermal regions by developing a group of mouse strains.

Read the full summary ↓

By integrating high-throughput and high-precision single-cell RNA sequencing with sophisticated imaging techniques across various mouse models, we comprehensively resolve the spatiotemporal and genetic lineage differentiation processes of the endoderm at a single-cell resolution. Our findings reveal a previously unrecognized multipotentiality within early endodermal regions for differentiation into diverse organ primordia. Furthermore, this research illuminates the complex and underestimated phenomenon of multiple origins in the development of endodermal organs, prompting a reevaluation of differentiation models for these organs. This work not only advances our understanding of developmental biology, but also has significant implications for regenerative medicine and the development of organoid models, providing new insights into the intricate mechanisms that guide organogenesis.

Published in

Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution

Li KR, Yu PL, Zheng QQ et al. · Cell 2025 · PMID 39824184 · doi:10.1016/j.cell.2024.12.012

This dataset

Open GSE277789 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 GSE277789_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 PRJNA1164201 and SRA study SRP534204. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39824184) ↗

Study design

830 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from the first 400 of 830 sample titles: 400 distinct titles with little repetition. 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

GSM8529766 Endoderm Ngn3Cre 18ss b2 001, scRNA-seq
GSM8529767 Endoderm Ngn3Cre 18ss b2 002, scRNA-seq
GSM8529768 Endoderm Ngn3Cre 18ss b2 003, scRNA-seq
GSM8529769 Endoderm Ngn3Cre 21ss b2 001, scRNA-seq
GSM8529770 Endoderm Ngn3Cre 21ss b2 002, scRNA-seq
GSM8529771 Endoderm Ngn3Cre 21ss b2 003, scRNA-seq
GSM8529772 Endoderm Ngn3Cre 21ss b2 004, scRNA-seq
GSM8529773 Endoderm Ngn3Cre 21ss b2 005, scRNA-seq
GSM8529774 Endoderm Ngn3Cre 21ss b2 006, scRNA-seq
GSM8529775 Endoderm Ngn3Cre 21ss b2 007, scRNA-seq
GSM8529776 Endoderm Ngn3Cre 21ss b2 008, scRNA-seq
GSM8529777 Endoderm Ngn3Cre 21ss b2 009, scRNA-seq
GSM8529778 Endoderm Ngn3Cre 21ss b2 010, scRNA-seq
GSM8529779 Endoderm Ngn3Cre 21ss b2 011, scRNA-seq
GSM8529780 Endoderm Ngn3Cre 21ss b2 012, scRNA-seq
GSM8529781 Endoderm Ngn3Cre 21ss b2 013, scRNA-seq
GSM8529782 Endoderm Ngn3Cre 21ss b2 014, scRNA-seq
GSM8529783 Endoderm Ngn3Cre 21ss b2 015, scRNA-seq
GSM8529784 Endoderm Ngn3Cre 21ss b2 016, scRNA-seq
GSM8529785 Endoderm Ngn3Cre 21ss b2 017, scRNA-seq
GSM8529786 Endoderm Ngn3Cre 21ss b2 018, scRNA-seq
GSM8529787 Endoderm Ngn3Cre 21ss b2 019, scRNA-seq
GSM8529788 Endoderm Ngn3Cre 21ss b2 020, scRNA-seq
GSM8529789 Endoderm Ngn3Cre 21ss b2 021, scRNA-seq
GSM8529790 Endoderm Ngn3Cre 21ss b2 022, scRNA-seq
GSM8529791 Endoderm Ngn3Cre 21ss b2 023, scRNA-seq
GSM8529792 Endoderm Ngn3Cre 21ss b2 024, scRNA-seq
GSM8529793 Endoderm Ngn3Cre 21ss b2 025, scRNA-seq
GSM8529794 Endoderm Ngn3Cre 21ss b2 026, scRNA-seq
GSM8529795 Endoderm Ngn3Cre 21ss b2 027, scRNA-seq
GSM8529796 Endoderm Ngn3Cre 21ss b2 028, scRNA-seq
GSM8529797 Endoderm Ngn3Cre 21ss b2 029, scRNA-seq
GSM8529798 Endoderm Ngn3Cre 21ss b2 030, scRNA-seq
GSM8529799 Endoderm Ngn3Cre 21ss b2 031, scRNA-seq
GSM8529800 Endoderm Ngn3Cre 21ss b2 032, scRNA-seq
GSM8529801 Endoderm Ngn3Cre 21ss b2 033, scRNA-seq
GSM8529802 Endoderm Ngn3Cre 21ss b2 034, scRNA-seq
GSM8529803 Endoderm Ngn3Cre 21ss b2 035, scRNA-seq
GSM8529804 Endoderm Ngn3Cre 21ss b2 036, scRNA-seq
GSM8529805 Endoderm Ngn3Cre 21ss b2 037, scRNA-seq

+ 790 more — browse all 830 samples with per-sample file links →

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Search all mouse 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.