Dense transcript profiling in single cells by image correlation decoding
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Updated: Mar 19, 2026

Single Cell Analysis Of Transcriptionally Active Alleles By Single Molecule FISH
Published on: September 20, 2020
Ahmet F Coskun1,2, Long Cai1,2
1Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA.
Abstract:
Sequential barcoded fluorescent in situ hybridization (seqFISH) allows large numbers of molecular species to be accurately detected in single cells, but multiplexing is limited by the density of barcoded objects. We present correlation FISH (corrFISH), a method to resolve dense temporal barcodes in sequential hybridization experiments. Using corrFISH, we quantified highly expressed ribosomal protein genes in single cultured cells and mouse thymus sections, revealing cell-type-specific gene expression.
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