Dense transcript profiling in single cells by image correlation decoding

Recent work in sequential fluorescent in-situ hybridization (FISH) has demonstrated the ability to uniquely encode a large number of molecular species in single cells. However, the multiplexing capacity is practically limited by the density of the barcoded objects in the cell. Here, we present a general method using image correlation to resolve the temporal barcodes in sequential hybridization experiments, allowing high density objects to be decoded. Using this correlation FISH (corrFISH) approach, we profiled the gene expression of ribosomal proteins in single cells in cell cultures and in mouse thymus tissue sections. In tissues, corrFISH revealed cell type specific gene expression of ribosomal proteins. The combination of sequential barcoding FISH and correlation analyses provides a general strategy for multiplexing a large number of RNA molecules and potentially other high copy number molecules in single cells.