Methods for determining a location of a biological analyte in a biological sample

A method for determining a location of a nucleic acid analyte within a biological sample, the method comprising:

• (a) providing an array comprising a plurality of capture probes immobilized on the substrate, wherein a capture probe of the plurality of capture probes comprises a spatial barcode and a capture domain;
• (b) contacting the biological sample with the substrate;
• (c) contacting a polymer material to the biological sample, and activating the polymer material to form a hydrogel-embedded biological sample
• (d) permeabilizing the hydrogel-embedded biological sample under conditions sufficient to allow the nucleic acid analyte within the biological sample to hybridize to a capture probe;
• and
• (e) determining the sequence of (i) the spatial barcode or a complement thereof and (ii) the sequence of the analyte, or a complement thereof and using the determined sequences of (i) and (ii) to determine the location of the nucleic acid analyte in the biological sample.