Three-dimensional intact-tissue sequencing of single-cell transcriptional states

TLDR

3D brain RNA sequencing captures the entire transcriptome but loses anatomical context, whereas in situ hybridization is limited to a few transcripts, and in situ sequencing offers a solution yet struggles in dense, complex tissues. The authors aim to develop a multidisciplinary 3D intact-tissue RNA sequencing method by combining efficient sequencing with hydrogel‑tissue chemistry. They integrated an efficient sequencing approach with hydrogel‑tissue chemistry to enable 3D intact‑tissue RNA sequencing. The method mapped over 1,000 genes at single‑cell resolution in mouse brain sections, delineating cell types, circuit states, and organizational principles. Published in Science (issue p.

Abstract

Transcriptome mapping in the 3D brain RNA sequencing samples the entire transcriptome but lacks anatomical information. In situ hybridization, on the other hand, can only profile a small number of transcripts. In situ sequencing technologies address these shortcomings but face a challenge in dense, complex tissue environments. Wang et al. combined an efficient sequencing approach with hydrogel-tissue chemistry to develop a multidisciplinary technology for three-dimensional (3D) intact-tissue RNA sequencing (see the Perspective by Knöpfel). More than 1000 genes were simultaneously mapped in sections of mouse brain at single-cell resolution to define cell types and circuit states and to reveal cell organization principles. Science , this issue p. eaat5691 ; see also p. 328