Developmental Research
Reveals Spatial Organization During Embryonic and Organ Development
Stereo-seq offers a unique approach to study tissue architecture and cellular diversity during embryonic and organ development. By preserving spatial information, it allows researchers to identify distinct cell populations, developmental niches, and their spatial relationships.
This approach supports the study of cell-fate determination, lineage differentiation, organogenesis, and tissue maturation. Furthermore, Stereo-seq enables the reconstruction of developing embryos and organs, helping researchers uncover the molecular programs and cellular interactions that shape functional tissues.
12
Peer-Reviewed Studies
5+
Species & Model Systems
Overview
Development unfolds across both space and time. Cell states emerge within precise anatomical neighborhoods, signalling centers guide lineage decisions, and coordinated tissue interactions shape the developing body. When samples are dissociated, these essential relationships are lost.
Stereo-seq preserves native tissue architecture while capturing whole-transcriptome information across large tissue sections. Researchers can examine complete developmental landscapes—from early lineage specification and body-plan formation to organ maturation, tissue regeneration and repair.
Map complete embryos and organs within a continuous spatial coordinate system.
Resolve cell-state transitions and lineage-associated programs in their native tissue context.
Reconstruct developmental processes across serial sections, stages and biological scales.
Integrate spatial transcriptomics with single-cell and multi-omics datasets.
Research Themes Covered
Embryogenesis & Organogenesis
Cell Fate, Differentiation & Multi-omics
Regeneration & Tissue Repair
Research Themes
Publications span three connected areas of developmental biology—from embryo and organ formation to cell-fate regulation and tissue regeneration.
01 — Embryogenesis
Embryogenesis & Organogenesis
Reconstruct intact embryos and emerging organ systems in two and three dimensions, revealing spatially coordinated lineage specification, signalling centers and early body-plan formation.
02 — Cell Fate
Cell Fate, Differentiation & Multi-omics
Trace how cells acquire identity across developmental time by integrating spatial transcriptomics with single-cell, chromatin-accessibility and other molecular measurements.
03 — Regeneration
Regeneration & Tissue Repair
Map the cellular programs and tissue microenvironments that support regeneration, wound healing and structural restoration across organs and model systems.
Featured Publications
Twelve peer-reviewed studies demonstrate how Stereo-seq resolves developmental processes across species, stages and biological scales.
How can early mouse organogenesis be reconstructed across an intact embryo rather than isolated regions?
Which spatial relationships coordinate primordium formation and signalling across germ layers?
Whole-embryo spatial profiling within a shared anatomical coordinate system.
Near single-cell spatial resolution across serial sections.
Supports three-dimensional reconstruction of developing structures and cell states.
Profiling 285 serial sections from six E7.5–E8.0 embryos generated full spatiotemporal transcriptome and signalling maps at single-cell resolution.
The SEU-3D framework reconstructed digital embryos and mapped endoderm and mesoderm derivatives together with cross-germ-layer signalling networks.
A primordium determination zone was identified at the anterior embryonic–extraembryonic interface at E7.75, where coordinated signalling contributes to cardiac primordium formation.
TakeawayStereo-seq enabled whole-embryo 3D reconstruction at single-cell resolution and revealed a spatial signalling hub associated with early cardiac primordium formation.
How do cell types and regulatory programs change across the development of a complete model organism?
Which molecular regulators coordinate spatially organized cell differentiation?
Maps developmental states across a complete organism in three dimensions and over time.
Integrates spatial information with single-cell transcriptomic and chromatin-accessibility data.
Connects regulatory programs to the anatomical locations in which differentiation occurs.
Flysta3D-v2 spans Drosophila development from embryo to pupa and integrates single-cell 3D spatial transcriptomics, scRNA-seq and scATAC-seq.
Multimodal integration produced developmentally continuous in silico 3D models and tissue trajectories that resolve cell-type differentiation.
Midgut-focused analysis identified regulatory transcription factors and experimentally validated exex as a key regulator of copper-cell development.
TakeawayStereo-seq connected developmental trajectories, chromatin regulation and 3D anatomy across the Drosophila life cycle.
How are early human lineages and signalling centers organized within an intact gastrulating embryo?
How can serial tissue sections be integrated into a coherent three-dimensional developmental reference?
Preserves spatial relationships across an intact Carnegie stage 8 human embryo.
Supports 3D reconstruction from serial sections.
Maps lineage trajectories and signalling centers to precise anatomical regions.
High-resolution spatial profiling captured 38,562 spots across 62 transverse sections and reconstructed an intact Carnegie stage 8 human embryo in 3D.
The study resolved embryonic and extra-embryonic lineage trajectories, associated regulons and spatially ordered mesoderm subtypes along the body axes.
It identified a potential signalling center at the posterior end of the embryo and mapped dynamic pathway activity supporting lineage progression and tissue patterning.
TakeawayStereo-seq reconstructed an intact human gastrula in 3D, linking early lineage programs and signalling activity to precise anatomical coordinates.
How are maternal and fetal cell states organized at the normal human maternal–fetal interface?
Which spatial programs support trophoblast invasion and vascular remodelling?
Maps cell states together with tissue architecture across spatially resolved biopsies.
Supports multimodal analysis of interacting maternal and fetal compartments.
Preserves the structural context needed to study invasion and vascular organization.
Integrated snRNA-seq and snATAC-seq supported a bistable regulatory model in which progenitor villous cytotrophoblasts commit to mutually exclusive extravillous or syncytiotrophoblast fates.
Submicrometre Stereo-seq maps from 16 second-trimester basal-plate biopsies resolved trophoblast invasion, spiral-artery remodelling and transient endothelial-state transitions in native tissue.
Integration with pregnancy-complication GWAS data linked fetal extravillous trophoblasts to pre-eclampsia risk and identified POU5F1+LGR5+ endometrial epithelial cells with shared risk enrichment.
TakeawayStereo-seq resolved trophoblast fate, vascular remodelling and genetically vulnerable cell populations across the human maternal–fetal interface.
How do epidermal and dermal interactions shape rete-ridge morphogenesis?
Are the underlying developmental mechanisms conserved across mammalian species?
Links gene-expression programs to emerging skin architecture.
Resolves spatial interactions between epidermal and dermal compartments.
Supports cross-species comparison of tissue morphogenesis.
Rete ridges were documented across mammalian species, including grizzly bears and dolphins, and neonatal pig wounds were shown to regenerate them de novo.
Multispecies spatiotemporal transcriptomics identified epidermal–dermal signalling interactions during rete-ridge morphogenesis, with a central role for BMP signalling.
Mouse fingerpad experiments demonstrated that epidermal BMP signalling is functionally required, supporting a rete-ridge program distinct from hair-follicle and sweat-gland formation.
TakeawayStereo-seq helped reveal a BMP-dependent, evolutionarily distinct program that builds and can regenerate mammalian rete-ridge architecture.
Which regulatory programs limit regenerative capacity in mammals?
Can a disabled genetic switch be reactivated to improve tissue regeneration?
Comparative single-cell and spatial transcriptomics mapped regenerative programs in rabbit and mouse pinna after injury.
Spatial context connected retinoic-acid production and degradation programs with regenerative and non-regenerative tissue states.
Cross-species analysis enabled comparison of active and evolutionarily inactivated Aldh1a2-linked regulatory elements.
Insufficient retinoic-acid production—caused by deficient Aldh1a2 and increased retinoic-acid degradation—was associated with failed mouse pinna regeneration.
Activating Aldh1a2 or supplementing retinoic acid reactivated regeneration.
A single rabbit enhancer driving Aldh1a2 was sufficient to improve ear-pinna regeneration in transgenic mice.
TakeawayComparative spatial genomics identified an evolutionarily disabled Aldh1a2–retinoic-acid switch that can be reactivated to improve mammalian tissue regeneration.
How are early mesodermal and extraembryonic cell states spatially organized in a Carnegie stage 7 human embryo?
Where do early germ-cell and haematopoietic programs emerge?
Generates a 3D spatial transcriptomic map of an intact early human embryo.
Resolves rare developmental states in their anatomical context.
Provides a reference for evaluating stem-cell-derived embryo models.
Stereo-seq profiling of 82 serial cryosections reconstructed a fully intact Carnegie stage 7 human embryo in three dimensions at single-cell resolution.
The atlas resolved early specification of distinct mesoderm subtypes and identified the anterior visceral endoderm.
Primordial germ cells were localized to the connecting stalk, while haematopoietic stem-cell-independent haematopoiesis was observed in the yolk sac.
TakeawayStereo-seq mapped rare, transient mesodermal, germ-cell and haematopoietic states across an intact Carnegie stage 7 human embryo.
How is the early human body plan organized during the transition from gastrulation to organogenesis?
Which cell states and structures define the Carnegie stage 9 embryo?
Reconstructs early body-plan structures in three dimensions.
Preserves the anatomical relationships between emerging tissues and cell states.
Provides a spatial reference for human-development and embryo-model research.
Spatial profiling of 75 transverse cryosections generated a 3D model containing brain and spinal regions, primitive gut, successive somite stages, and somatic and splanchnic mesoderm.
The study identified two hindbrain developmental trajectories, localized the isthmic organizer at the midbrain–hindbrain boundary and described a bilayered organization of neuromesodermal progenitors.
It also characterized early aorta formation and localized primordial germ cells in the aorta–gonad–mesonephros region.
TakeawayStereo-seq captured early human body-plan formation in 3D, resolving neural, mesodermal, vascular and germ-cell organization at the onset of organogenesis.
Do regenerative neural retinal stem-like cells exist in the human fetal retina?
Can their identity and regenerative potential be validated across spatial, organoid and transplantation models?
Localizes candidate retinal stem-like cells within developing retinal tissue.
Integrates spatial transcriptomics with single-cell multi-omics.
Connects native tissue location with organoid and transplantation evidence.
A distinct human neural retinal stem-like cell population was identified in the peripheral fetal retina within the ciliary marginal zone.
Human retinal organoids contained a transcriptionally similar population with comparable developmental trajectories; MECOM was identified as a regulator of neural-retinogenesis commitment and organoid repair.
Organoid-derived stem-like cells integrated after transplantation into rd10 retinitis-pigmentosa mice, alleviated retinal degeneration and improved visual function.
TakeawayStereo-seq localized a distinct human retinal stem-like cell population and connected its native developmental niche with organoid and transplantation evidence of regenerative potential.
How does 20E signalling reorganize cell states during silkworm wing-disc development?
Which spatial programs coordinate developmental reprogramming in an insect organ?
Maps single-cell states back into the spatial organization of the wing disc.
Resolves hormone-driven developmental changes across tissue regions.
Extends spatial developmental biology to an agriculturally relevant model organism.
A ten-timepoint atlas identified 12 major wing-disc cell types, with wing-morphogenesis cells acting as central progenitors for epithelial and cuticle lineages.
Differentiation trajectories were associated with regulators including Rfx, Blimp-1, Dll and Pur-alpha, while wing-morphogenesis cells functioned as early signalling hubs.
20-hydroxyecdysone rapidly compressed developmental time by accelerating fate transitions and gene-expression changes; the authors summarized this progression in a five-stage Gene Transition Model.
TakeawayStereo-seq revealed how 20-hydroxyecdysone reorganizes cell fate, signalling and tissue patterning across silkworm wing development.
How do cellular states and tissue programs change across the full course of heart regeneration?
Which anatomical regions coordinate repair across successive regenerative stages?
Captures whole-organ spatial context across eight regenerative stages.
Connects changing cell states with precise regions of the regenerating heart.
Supports reconstruction of temporal and spatial regeneration trajectories.
Integrated Stereo-seq and scRNA-seq across eight stages defined a cascade of cardiomyocyte states that produces regenerated myocardium.
The atlas suggested a role for tpm4a in cardiomyocyte re-differentiation and identified activation of ifrd1 and atp6ap2 as features of regenerative hearts.
The study reconstructed a four-dimensional virtual regenerating heart containing 569,896 cells or spots from 36 scRNA-seq libraries and 224 Stereo-seq slices.
TakeawayStereo-seq delivered an organ-wide, eight-stage view of cardiomyocyte-state transitions and molecular programs coordinating zebrafish heart regeneration.
How is fibroblast heterogeneity organized during wound healing and scar formation?
What role does Gb3 play in coordinating spatially distinct repair programs?
Maps fibroblast states across space and healing time.
Connects molecular variation with specific wound and scar regions.
Provides a spatial framework for exploring pathological scarring and chronic-wound pathways.
Gb3 biosynthesis was higher in superficial second-degree burns than in deep second-degree burns, and HEXB was identified as the distinguishing Gb3-synthesis enzyme.
Suppressing HEXB-mediated Gb3 synthesis increased fibroblast-to-myofibroblast transition, weakened FGF2 signalling and increased fibrotic scarring in experimental models.
The study proposed a HEXB–Gb3–FGF2 regulatory axis in which Gb3 supports papillary and fibrolytic fibroblast states and limits excessive collagen deposition.
TakeawayStereo-seq linked depth-dependent Gb3 metabolism to fibroblast-state changes and identified a HEXB–Gb3–FGF2 axis associated with wound repair and scar formation.
Why developmental researchers choose Stereo-seq?
Four capabilities make Stereo-seq uniquely suited to studying development across space, time and biological scale.
Whole-embryo and whole-organ coverage
Profile continuous developmental landscapes in a single experiment—from complete embryos and organ systems to signalling centers, tissue boundaries and emerging anatomical structures.
Near single-cell spatial resolution
Distinguish neighboring cell states, rare developmental populations and localized lineage programs while preserving their native tissue relationships.
Spatiotemporal and 3D reconstruction
Integrate serial sections and developmental stages to reconstruct changing tissue architecture, cell-state transitions and body-plan formation in two and three dimensions.
Multi-omics and model-system versatility
Combine spatial transcriptomics with single-cell and multi-omics measurements across human samples and established model organisms, enabling comparative and mechanistic studies.