Embryo-scale, single-cell spatial transcriptomics-Reference-Cited by-同舟云学术

Embryo-scale, single-cell spatial transcriptomics

Published:2021-07-02 Issue:6550 Volume:373 Page:111-117
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Srivatsan Sanjay R.¹^ORCID,Regier Mary C.²³^ORCID,Barkan Eliza¹⁴^ORCID,Franks Jennifer M.¹^ORCID,Packer Jonathan S.⁵^ORCID,Grosjean Parker²^ORCID,Duran Madeleine¹^ORCID,Saxton Sarah²^ORCID,Ladd Jon J⁶,Spielmann Malte⁷⁸^ORCID,Lois Carlos⁹^ORCID,Lampe Paul D.⁶^ORCID,Shendure Jay¹¹⁰¹¹¹²^ORCID,Stevens Kelly R.²³¹²¹³^ORCID,Trapnell Cole¹¹⁰¹²^ORCID

Affiliation:

1. Department of Genome Sciences, University of Washington, Seattle, WA, USA.

2. Department of Bioengineering. University of Washington, Seattle, WA, USA.

3. Institute for Stem Cell and Regenerative Medicine, Seattle, WA, USA.

4. Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.

5. Foresite Labs, Boston, MA, USA.

6. Translational Research Program, Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

7. Institute of Human Genetics, University of Lübeck, Lübeck, Germany.

8. Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, Berlin, Germany.

9. Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.

10. Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.

11. Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.

12. Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.

13. Department of Laboratory Medicine and Pathology, Seattle, WA, USA.

Abstract

Localizing gene expression Single-cell RNA sequencing can provide information about cellular relationships based on shared transcriptomes, but most methods lose spatial information. Those methods that do retain spatial information can be limited to a specific set of genes and/or a small area. Srivatsan et al. introduce sci-Space, a spatial transcriptomic method that uses a grid of barcoded oligos on a slide that can be transferred to nuclei of an overlaid frozen tissue section to obtain both the spatial origin and the transcriptome of thousands of single cells per slide. The researchers used sci-Space to create a spatial atlas of mouse E14 sagittal sections, revealing spatially expressed genes across cell types. This application illustrates how sci-Space complements existing approaches in spatial genomics. Science , abb9536, this issue p. 111

Funder

Howard Hughes Medical Institute

NIH Office of the Director

Washington Research Foundation

Paul G. Allen Family Foundation

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

Reference42 articles.

1. The single-cell transcriptional landscape of mammalian organogenesis

2. A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution