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Brief Communication

Nature Methods 2, 663–665 (1 September 2005) | doi:10.1038/nmeth786

Gene expression profiling in single cells within tissue

Paola Capodieci , Michael Donovan , Heidi Buchinsky , Yusuf Jeffers , Carlos Cordon-Cardo , William Gerald , Jon Edelson , Shailesh M Shenoy & Robert H Singer

We developed a robust multiplex fluorescent in situ hybridization (FISH) technique in archival formalin-fixed, paraffin-embedded (FFPE) human tissue sections while preserving the microanatomical context. This identifies single-cell gene expression patterns by probing multiple, unique nascent RNA transcripts and yields predictive quantitative gene expression signatures.