Detection and quantification of analytes, such as nucleic acids, provide diagnostic information in disease. One class of nucleic acid analyte is miRNAs, small RNA molecules that regulate gene expression in cells. The miRNA repertoire of cells is highly specific to cell-type, and miRNA expression is frequently dysregulated in diseases including cancer, sepsis, organ failure, autoimmune diseases, and neurodegenerative diseases. miRNAs are therefore an attractive diagnostic and prognostic target, however, current miRNA quantitation techniques are expensive, labor intensive, and often lack multiplexed readings or high throughput capacity. These challenges in miRNA detection and quantification have thus far hindered the adoption of miRNA markers as a diagnostic or prognostic tool in the clinic. These inventors developed a novel assay that can be multiplexed and that greatly simplifies miRNA detection. In another embodiment, the technology can be used to detect analytes from stained and preserved clinical tissue sections.