Spatial analysis of epigenetic modifications

A method for identifying methylation status of an analyte in a biological sample, the method comprising:

• (a) contacting the biological sample with an array comprising a plurality of capture probes, wherein a capture probe in the plurality of capture probes comprises (i) a spatial barcode and (ii) a capture domain comprising at least one methylated cytosine;
• (b) deaminating the analyte in the biological sample;
• (c) contacting the analyte with a plurality of probes comprising a first probe and a second probe, wherein
• the first probe comprises (i) a sequence complementary to at least a first sequence of the analyte and (ii) a sequence complementary to the capture domain;
• and
• the second probe comprises a sequence complementary to at least a second sequence of the analyte;
• (d) ligating the first probe and the second probe, thereby generating a ligation product;
• (e) hybridizing the ligation product to the capture probe;
• (f) extending the capture probe using the ligation product as a template;
• thereby generating an extended capture probe;
• and
• (g) determining (i) all or a portion of the sequence of the spatial barcode or the complement thereof, and (ii) all or a portion of the sequence of the extended capture probe, or a complement thereof, and using the determined sequences of (i) and (ii) to identify the methylation status of the analyte in the biological sample.