Museum of spatial transcriptomics

• Published in: Nature methods Vol. 19; no. 5; pp. 534 - 546
• Main Authors: Moses, Lambda, Pachter, Lior
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.05.2022; Nature Publishing Group
• Subjects: 631/114/794; 631/1647/2017/1947; 631/1647/514/1949; 631/1647/794; Bioinformatics; Biological Microscopy; Biological Techniques; Biomedical and Life Sciences; Biomedical Engineering/Biotechnology; Computer applications; Data processing; Embryos; Gene expression; Life Sciences; Literature reviews; Proteomics; Review Article; Spatial data; Transcriptomics; Tumors
• ISSN: 1548-7091; 1548-7105; 1548-7105
• DOI: 10.1038/s41592-022-01409-2

The function of many biological systems, such as embryos, liver lobules, intestinal villi, and tumors, depends on the spatial organization of their cells. In the past decade, high-throughput technologies have been developed to quantify gene expression in space, and computational methods have been developed that leverage spatial gene expression data to identify genes with spatial patterns and to delineate neighborhoods within tissues. To comprehensively document spatial gene expression technologies and data-analysis methods, we present a curated review of literature on spatial transcriptomics dating back to 1987, along with a thorough analysis of trends in the field, such as usage of experimental techniques, species, tissues studied, and computational approaches used. Our Review places current methods in a historical context, and we derive insights about the field that can guide current research strategies. A companion supplement offers a more detailed look at the technologies and methods analyzed: https://pachterlab.github.io/LP_2021/ . This work presents an overview of the evolution of spatial transcriptomics and highlights recent efforts in method developments in this space.