Integrating Single-cell and Spatial Transcriptomics to Elucidate Intercellular Tissue Dynamics

Overview

Journal Nat Rev Genet

Specialty Genetics

Date 2021 Jun 19

PMID 34145435

Citations 330

Authors

Sophia K Longo

Margaret G Guo

Andrew L Ji

Paul A Khavari

Affiliations

Soon will be listed here.

Abstract

Single-cell RNA sequencing (scRNA-seq) identifies cell subpopulations within tissue but does not capture their spatial distribution nor reveal local networks of intercellular communication acting in situ. A suite of recently developed techniques that localize RNA within tissue, including multiplexed in situ hybridization and in situ sequencing (here defined as high-plex RNA imaging) and spatial barcoding, can help address this issue. However, no method currently provides as complete a scope of the transcriptome as does scRNA-seq, underscoring the need for approaches to integrate single-cell and spatial data. Here, we review efforts to integrate scRNA-seq with spatial transcriptomics, including emerging integrative computational methods, and propose ways to effectively combine current methodologies.

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