← BioTransfer GEO Dataset Finder
GEO series

Unraveling Enteroendocrine Cell lineage dynamics and associated gene regulatory networks during intestinal development

GSE306837 Mus musculus (mouse) Single-cell RNA-seq 13 samples Submitted 2025/09/05 Platform GPL19057Platform GPL18573
At a glance

Single-cell RNA-seq · mouse · 13 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
13 samples: 3 × FACS sorted eYFP+ EECs from E18.5 mSI, plate IGB-AA-s vs 3 × FACS sorted Venus+ EECs from tHIOs, plate IGB-AA-s vs 2 × FACS sorted eYFP+ EECs from P12 mSI, plate IGB-AA-s vs 2 × FACS sorted Venus+ EECs from HIOs, plate IGB-AA-sGroups 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
Unraveling enteroendocrine cell lineage dynamics and associated gene regulatory networks during intestinal developmentBiology open · 2025
Summary (written by the submitters)
Enteroendocrine cells (EECs) are rare intestinal epithelial cells producing multiple hormones that regulate essential aspects of digestion and energy. EEC subtypes, their hormone repertoire and differentiation mechanisms from intestinal stem cells have been characterized in the adult intestine. However, the mechanisms underlying EEC subtype specification during development are largely unknown.
Read the full summary ↓
We characterized EEC lineages and their dynamics during development using both genetically modified mouse and human models (i.e. human intestinal organoids, HIOs, derived from induced pluripotent stem cells and transplanted HIOs, tHIOs), which we analyzed by single-cell RNA sequencing using plate-based SORT-seq technology. Our findings demonstrate that in both mice and humans, the majority of EECs are specified during development through similar differentiation trajectories as observed in the adult intestine. This suggests that EEC subtypes specification occurs independently of fully organized crypt-villus structures and stimulation by diet or microbiota. However, the emergence of certain EEC subtypes depends on tissue maturation. Finally, our integrative approach infers lineage-specific regulators dynamically, identifying new candidates controlling EEC differentiation in the developing human gut.
Published in
Unraveling enteroendocrine cell lineage dynamics and associated gene regulatory networks during intestinal development
Jiménez S, Blot F, Meunier A et al. · Biology open 2025 · PMID 41117135 · doi:10.1242/bio.062083
This dataset
Open GSE306837 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 GSE306837_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 PRJNA1312485 and SRA study SRP614649. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41117135) ↗
Study design
3 × FACS sorted eYFP+ EECs from E18.5 mSI, plate IGB-AA-s vs 3 × FACS sorted Venus+ EECs from tHIOs, plate IGB-AA-s vs 2 × FACS sorted eYFP+ EECs from P12 mSI, plate IGB-AA-s vs 2 × FACS sorted Venus+ EECs from HIOs, plate IGB-AA-s

Supports a between-group comparison across 10 samples.

How we read this: 4 replicated groups read from 13 sample titles; they account for 10 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

Search all RNA-seq datasets in GEO →

Share this dataset

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.