Three‐dimensional in situ sequencing of single cells in intact tissue

Abstract

Conventional sequencing methods are unable to measure sequence and spatial information simultaneously, limiting our understanding of the spatial heterogeneity of molecules within cells and intact tissues. To address this issue, multiplexed in situ hybridization and a new generation of sequencing methods termed in situ sequencing have emerged, aiming to spatially resolve RNAs inside cells. Such spatial transcriptomic profiling is critical to resolving cell identity in intact issues, a key question in neuroscience today as the brain consists of a three‐dimensional (3D) tapestry of cell types whose functional diversity arises from the spatial heterogeneity of gene expression. We developed a 3D intact‐tissue RNA sequencing technique in complex organs, termed STARmap, enabling targeted single‐cell gene expression mapping via in situ sequencing within mouse cortex. This new analytical approach has great promises for addressing a series of fundamental questions in neuroscience (e.g. spatial organization of cell types, molecular markers of functional circuits, activity‐triggered gene expression) that are hard to be studied otherwise.Support or Funding InformationX.W. is supported by a Life Science Research Foundation fellowship and the Gordon and Betty Moore Foundation. W.E.A. is supported by a Fannie and John Hertz Foundation Fellowship and an NSF Graduate Research Fellowship. K.D. is supported by NIMH (R01MH099647), NIDA (P50DA042012), the DARPA NeuroFAST program W911NF‐14‐2‐0013, the NSF NeuroNex program, the Gatsby Foundation, the AE Foundation, the NOMIS Foundation, the Fresenius Foundation, the Wiegers Family Fund, the James Grosfeld Foundation, the Sam and Betsy Reeves Foundation, and the HL Snyder Foundation.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.