Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays

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.

Keywords

Affiliated Institutions

• Spanish National Centre for Cardiovascular Research ES
• Science for Life Laboratory SE
• Chinese Academy of Sciences CN
• Guangzhou Institutes of Biomedicine and Health CN
• Shenzhen Bay Laboratory CN
• University of Cambridge GB
• Massachusetts Institute of Technology US
• Institució Catalana de Recerca i Estudis Avançats ES
• Medical Research Council GB
• Institute of Genetics and Developmental Biology CN
• BGI Genomics
• KTH Royal Institute of Technology SE
• BGI Group (China) CN
• University of Chinese Academy of Sciences CN
• Guangdong Academy of Medical Sciences CN
• China National GeneBank CN
• University of Oxford GB
• Howard Hughes Medical Institute US
• Whitehead Institute for Biomedical Research US
• University of Copenhagen DK
• Guangdong Provincial People's Hospital CN
• Zhengzhou University CN
• Universitat Pompeu Fabra ES
• Karolinska Institutet SE

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