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Srivatsan SR, Regier MC, Barkan E, Franks JM, Packer JS, Grosjean P, Duran M, Saxton S, Ladd JJ, Spielmann M, Lois C, Lampe PD, Shendure J, Stevens KR, Trapnell C. Embryo-scale, single-cell spatial transcriptomics. Science 2021; 373:111-117. [PMID: 34210887 PMCID: PMC9118175 DOI: 10.1126/science.abb9536] [Citation(s) in RCA: 133] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 02/13/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022]
Abstract
Spatial patterns of gene expression manifest at scales ranging from local (e.g., cell-cell interactions) to global (e.g., body axis patterning). However, current spatial transcriptomics methods either average local contexts or are restricted to limited fields of view. Here, we introduce sci-Space, which retains single-cell resolution while resolving spatial heterogeneity at larger scales. Applying sci-Space to developing mouse embryos, we captured approximate spatial coordinates and whole transcriptomes of about 120,000 nuclei. We identify thousands of genes exhibiting anatomically patterned expression, leverage spatial information to annotate cellular subtypes, show that cell types vary substantially in their extent of spatial patterning, and reveal correlations between pseudotime and the migratory patterns of differentiating neurons. Looking forward, we anticipate that sci-Space will facilitate the construction of spatially resolved single-cell atlases of mammalian development.
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Affiliation(s)
- Sanjay R Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Mary C Regier
- Department of Bioengineering. University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA, USA
| | - Eliza Barkan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Jennifer M Franks
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Parker Grosjean
- Department of Bioengineering. University of Washington, Seattle, WA, USA
| | - Madeleine Duran
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sarah Saxton
- Department of Bioengineering. University of Washington, Seattle, WA, USA
| | - Jon J Ladd
- Translational Research Program, Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Malte Spielmann
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Carlos Lois
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Paul D Lampe
- Translational Research Program, Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Kelly R Stevens
- Department of Bioengineering. University of Washington, Seattle, WA, USA.
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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