Methods for spatial analysis using rna-templated ligation

Abstract

Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

What is claimed is: 
     
         1 . A composition comprising:
 (a) a biological sample placed on a first substrate, wherein the biological sample comprises an analyte; and   (b) a second substrate comprising a spatial array comprising a plurality of capture probes affixed to the substrate, wherein a capture probe of the plurality of capture probes comprises (i) a spatial barcode comprising a sequence that provides a location of the analyte and (ii) a capture domain, wherein the first substrate is aligned with the second substrate, such that at least a portion of the biological sample is aligned with at least a portion of the spatial array;   (c) a ligation product comprising a first probe and a second probe, wherein the first probe and the second probe each comprise a sequence that is substantially complementary to a sequence of the analyte, and wherein one of the first probe or the second probe comprises a capture probe capture domain that is hybridized to the capture domain of the capture probe on the second substrate.