Gene expression profiling in single cells within tissue

Nat Methods. 2005 Sep;2(9):663-5. doi: 10.1038/nmeth786.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Biomarkers, Tumor / metabolism*
  • Gene Expression Profiling / methods*
  • Humans
  • In Situ Hybridization, Fluorescence / methods*
  • Male
  • Neoplasm Proteins / metabolism*
  • Paraffin Embedding / methods*
  • Prostatic Neoplasms / metabolism*
  • Prostatic Neoplasms / pathology*
  • Tissue Distribution
  • Tumor Cells, Cultured


  • Biomarkers, Tumor
  • Neoplasm Proteins