Museum of Spatial Transcriptomics

Author:

Moses LambdaORCID,Pachter LiorORCID

Abstract

AbstractThe 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 assess the ability and potential of spatial gene expression technologies to drive biological discovery, we present a curated database 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 analysis places current methods in 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/.

Publisher

Cold Spring Harbor Laboratory

Reference161 articles.

1. Liao, J. , Lu, X. , Shao, X. , Zhu, L. & Fan, X. Uncovering an Organ’s Molecular Architecture at Single-Cell Resolution by Spatially Resolved Transcriptomics. Trends in Biotechnology. ISSN: 01677799. https://linkinghub.elsevier.com/retrieve/pii/S0167779920301402 (June 2020).

2. Spatially Resolved Transcriptomes—Next Generation Tools for Tissue Exploration;BioEssays,2020

3. The Spatial and Genomic Hierarchy of Tumor Ecosystems Revealed by Single-Cell Technologies;Trends in Cancer,2019

4. Lein, E. , Borm, L. E. & Linnarsson, S. The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing 2017.

5. Single-cell genomics and spatial transcriptomics: Discovery of novel cell states and cellular interactions in liver physiology and disease biology;Journal of Hepatology,2020

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