US Patent 11981958 Methods for spatial analysis using DNA capture

Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using DNA templated ligation. For example, provided herein are methods for detecting an gDNA analyte in a biological sample where (i) the first RTL probe and second RTL probe hybridize to adjacent sequences on the gDNA analyte, (ii) enzyme-mediate cleavage of a 5′ FLAP results in release of the 5′ FLAP, and (iii) the sequence of the 5′ FLAP is determined and used to detect the gDNA analyte in the biological sample.