Methods of using master / copy arrays for spatial detection

A method of identifying a location of a biological analyte in a biological sample comprising:

• (a) providing a substrate comprising a plurality of capture probes, wherein a capture probe of the plurality of capture probes comprises a spatial barcode and a capture domain;
• (b) contacting the substrate with a plurality of analyte capture agents, wherein an analyte capture agent of the plurality of analyte capture agents comprises an analyte binding moiety and a capture agent barcode domain, and the capture probe binds to the analyte capture agent via the capture domain of the capture probe;
• (c) producing a spatially-tagged analyte capture agent, by extending the capture agent barcode domain to include a sequence that is complementary to the spatial barcode of the capture probe;
• (d) labelling a cell of the biological sample with one or more spatially-tagged analyte capture agents, by contacting the one or more spatially-tagged analyte capture agents with the biological sample, wherein at least one spatially-tagged analyte capture agent interacts with the biological analyte within the biological sample, and denaturing the spatially-tagged analyte capture agent from the capture probe;
• (e) dissociating the biological sample into a plurality of cells, wherein the at least one spatially-tagged analyte capture agent is associated with a dissociated cell;
• and
• (f) using the at least one spatially-tagged analyte capture agent to identify the location of the target biological analyte in the biological sample.