Spatially encoded biological assays

A method for determining a location of a protein and a nucleic acid in a biological sample, the method comprising:

• (a) contacting the biological sample with a binding agent that specifically binds to the protein, wherein the binding agent is coupled to an oligonucleotide comprising a sequence;
• (b) contacting the biological sample with an array comprising a first capture probe and a second capture probe, wherein:
• the first capture probe comprises (i) a first target-binding domain that hybridizes to the oligonucleotide coupled to the binding agent, and (ii) a nucleic acid sequence that identifies a unique location of the first capture probe on the array;
• and
• the second capture probe comprises (i) a second target-binding domain that hybridizes to the nucleic acid of the biological sample, and (ii) a nucleic acid sequence that identifies the unique location of the second capture probe on the array;
• (c) determining (i) a sequence of the oligonucleotide coupled to the binding agent, or a complement thereof, and (ii) the nucleic acid sequence that identifies the unique location of the first capture probe on the array, or a complement thereof, and using the determined sequences of (i) and (ii) to determine the location of the protein in the biological sample;
• and
• (d) determining (i) all or a portion of a sequence of the nucleic acid of the biological sample, or a complement thereof, and (ii) the nucleic acid sequence that identifies the unique location of the second capture probe on the array, or a complement thereof, and using the determined sequences of (i) and (ii) to determine the location of the nucleic acid in the biological sample.