GEO series

Lineage and Organ Signals Sequentially Build Organ Intrinsic Nervous Systems [scRNA-seq]

GSE322764 Mus musculus (mouse) Single-cell RNA-seq 19 samples Submitted 2026/03/16 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 19 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: 19 samples: 19 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: Lineage and organ signals sequentially build organ intrinsic nervous systemsNature · 2026

Summary (written by the submitters)

Organ intrinsic nervous systems (OINSs) are critical components of the body–brain axis, coordinating visceral organ function with systemic physiological control. Despite their importance, how these distinct neural architectures arise from a common neural crest cell (NCC) origin has remained unclear. Here, we present a systems-level, cross-organ analysis of OINS development, integrating lineage tracing, 3D imaging, single-cell transcriptomics, and genetic perturbations across heart, pancreas, intestine, and lungs.

Read the full summary ↓

We show that differences in NCC migratory trajectories prefigure the spatial architecture of OINSs, laying the foundation for organ-specific patterning. In contrast, molecular identity emerges largely in response to local environments, indicating that extrinsic cues play a major instructive role. Using in vitro co-cultures, we demonstrate that organ-derived cues reprogram intrinsic neurons toward organ-specific transcriptional profiles and direct neuronal differentiation, with extracellular matrix (ECM) contact identified as a central mediator. In vivo, ECM–integrin signaling supports intrinsic cardiac neuron neurogenesis, while ECM crosslinking stabilizes their stereotyped ganglionic organization. Together, these findings reveal that OINS diversity arises through a dual logic: lineage programs prefigure spatial frameworks, while organ-specific cues instruct final molecular identities and architectural precision. This work establishes a conceptual paradigm for how organs actively build their own nervous systems, illuminating principles that underpin body–brain integration.

Published in

Lineage and organ signals sequentially build organ intrinsic nervous systems

Hsu IY, Zhao J, Lin Y et al. · Nature 2026 · PMID 42129551 · doi:10.1038/s41586-026-10490-y

This dataset

Open GSE322764 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 GSE322764_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 PRJNA1431444 and SRA study SRP680734. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42129551) ↗

Study design

19 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 19 sample titles: 19 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

GSM9558094 061821ICNE12_5
GSM9558095 062521ICNE12_5
GSM9558096 101122_ICN_E14_5
GSM9558097 052721ICNE14_5_1
GSM9558098 102522ICNE16_5
GSM9558099 020921ICNE18_5
GSM9558100 021320_ICNP56
GSM9558101 090622ICN_Near_E14_5
GSM9558102 090622ICN_Far_E14_5
GSM9558103 070623_E14.5_Gut
GSM9558104 070623_E14.5_ENS
GSM9558105 Lung_Phox2b_011824
GSM9558106 Pancreas_Phox2b_011824
GSM9558107 090523_ENSGut
GSM9558108 081423_ENSGut
GSM9558109 051923_ENSGut
GSM9558110 042023_ENSGut
GSM9558111 090523_ENSHeart
GSM9558112 051923_ENSHeart

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