Simultaneous quantification of gene expression in a user-defined region of a cross-sectioned tissue

A method of producing a spatially-resolved profile of nucleic acid abundance in a tissue sample comprising:

• a) contacting the tissue sample with a solution comprising at least 15 species of probes, the probes comprising a target-binding domain, a signal oligonucleotide, and a photo-cleavable motif located between the target-binding domain and the signal oligonucleotide,
• wherein each species of probe comprises a unique nucleic acid target-binding domain that hybridizes to one of the at least 15 target nucleic acids and a unique signal oligonucleotide specific for the target nucleic acid;
• b) illuminating a first location of the tissue sample with light sufficient to release signal oligonucleotides at the first location;
• c) collecting the signal oligonucleotides released in step (b) from the solution proximal to the first location;
• d) identifying and quantifying via multiplexed immunohistochemistry the signal oligonucleotides collected in step (c), thereby determining the abundance of the at least 15 target nucleic acids in the first location;
• e) illuminating at least a second location of the tissue sample with light sufficient to release the signal oligonucleotides at the at least second location;
• f) collecting the signal oligonucleotides released in step (e) from the solution proximal to the at least second location;
• g) identifying and quantifying via multiplexed immunohistochemistry the signal oligonucleotides collected in step (f), thereby determining the abundance of the at least 15 target nucleic acids in the at least second location;
• and
• h) comparing the abundance of the at least 15 target nucleic acids in the first location of the tissue sample to the abundance of the at least 15 target nucleic acids in the at least second location of the tissue sample, thereby generating a spatially-resolved profile of nucleic acid abundance in the tissue sample.