Spatially encoded biological assays

A method for spatially associating 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 a unique location of the second capture probe on the array;
• and
• (c) generating a sequence complementary to the oligonucleotide coupled to the binding agent using the first target-binding domain of the first capture probe hybridized to the oligonucleotide as a primer;
• and
• (d) generating a cDNA using the second target-binding domain of the second capture probe hybridized to the nucleic acid of the biological sample as a primer;
• thereby spatially-associating the protein and the nucleic acid in the biological sample.