Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays
2022/05/01 by Ao Chen, Sha Liao, Mengnan Cheng +66 · 37 citations
Biochemistry, Genetics and Molecular Biology · Engineering · #Cell Image Analysis Techniques #Microfluidic and Bio-sensing Technologies #Single-cell and spatial transcriptomics
paper · pdf · doi:10.1016/j.cell.2022.04.003
openalex publication_date 2022/05/01 · openalex created_date 2022/05/08 · openalex updated_date 2026/07/31
Abstract
Spatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the imbalance between resolution, gene capture, and field of view of current methodologies precludes their systematic application to analyze relatively large and three-dimensional mid- and late-gestation embryos. Here, we combined DNA nanoball (DNB)-patterned arrays and in situ RNA capture to create spatial enhanced resolution omics-sequencing (Stereo-seq). We applied Stereo-seq to generate the mouse organogenesis spatiotemporal transcriptomic atlas (MOSTA), which maps with single-cell resolution and high sensitivity the kinetics and directionality of transcriptional variation during mouse organogenesis. We used this information to gain insight into the molecular basis of spatial cell heterogeneity and cell fate specification in developing tissues such as the dorsal midbrain. Our panoramic atlas will facilitate in-depth investigation of longstanding questions concerning normal and abnormal mammalian development.
Citations
Cited by
- NiCo identifies extrinsic drivers of cell state modulation by niche covariation analysis
- Single cell resolved spatial immune repertoire unveils spatial heterogeneity of lymphoid aggregates in human immune disorders
- Spatial instruction of tissue immunity
- A comprehensive benchmarking for spatially resolved transcriptomics clustering methods across variable technologies, organs, and replicates
- A practical guide for choosing an optimal spatial transcriptomics technology from seven major commercially available options
- Adult regenerative defects arise from discordant scaling of signal dependent growth and patterning
- CytoSignal detects locations and dynamics of ligand–receptor signaling at cellular resolution from spatial transcriptomic data
- Whole-transcriptome-scale isoform-resolved spatial imaging of single cells in tissues
- Decoding neurodegeneration one cell at a time
- Unified mass imaging maps the lipidome of vertebrate development
- Macrophage diversity in cancer revisited in the era of single-cell omics
- Spatial Modeling of Tissues for Morphogenic Field Analysis
- Marsilea: An intuitive generalized visualization paradigm for complex datasets
- SpaNorm: spatially-aware normalisation for spatial transcriptomics data
- Spatial Transcriptomics: Biotechnologies, Computational Tools, and Neuroscience Applications
- Single‐cell insights into plant growth, adaptation, and evolution
- Comprehensive noise reduction in single-cell data with the RECODE platform
- Spatial transcriptomics of a parasitic flatworm provides a molecular map of drug targets and drug resistance genes
- Emerging Techniques in Spatial Multiomics: Fundamental Principles and Applications to Dermatology
- Temporal and spatial omics technologies for 4D profiling
- STExplore: An Integrated Online Platform for Comprehensive Analysis and Visualization of Spatial Transcriptomics Data
- Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics
- Spatial transcriptomics in cancer research and potential clinical impact: a narrative review
- Simultaneous spatial transcriptomics and morphology profiling as tools to explore how microglia change with age
- Single-cell and spatial omics reveal progressive loss of xylem developmental complexity across seed plants
- Spatial Transcriptomics of Developing Wheat Seed Reveals Concentric Gene Expression Zones and Subgenome Biased Expression of Key Genes
- Automated Integration of Multi-Slice Spatial Transcriptomics Data in 2D and 3D
- Spatiotemporal transcriptomic niches of complement pathway and serine protease inhibitor activation in aging and infection
- Decrypting cancer's spatial code: from single cells to tissue niches
- Immune-mediated cardiac development and regeneration
- Spatial transcriptomics in neuroscience
- Quantitative characterization of cell niches in spatially resolved omics data
- The pigment cell : molecular, biological, and clinical aspects
- The Evolution of Spatial Omics Technologies Introduces A Novel Avenue for Lung Cancer Research
- NeMO Analytics: a compendium of transcriptomic data for the exploration of neocortical development
- Spatial transcriptomics in bone research: navigating hype and hurdles
- Uncovering the genetic architecture of pungency, carotenoids, and flavor in <i>Capsicum chinense</i> via TWAS-mGWAS integration and spatial transcriptomics
- Mitochondrial Retrograde Signaling in <i>Arabidopsis thaliana</i> : heterogenous, spatial and polarised aspects
Related