Gene expression profiling in single cells within tissue

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Abstract

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.

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Figure 1: Detection of nascent RNA (transcription sites) in paraffin-embedded tissue.
Figure 2: Correlation of single-cell multigene expression profiles with diagnostic pathology.
Figure 3: A combinatorial analysis of five genes provides a gene expression signature for each state.

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Acknowledgements

This work was supported in part by US National Institutes of Health CA-R33-083208 and by Aureon Laboratories.

Author information

Correspondence to Paola Capodieci or Robert H Singer.

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Competing interests

R.H.S. and C.C.-C. are scientific cofounders of Aureon Laboratories.

Supplementary information

Supplementary Table 1

Sequences used to generate probes. (PDF 46 kb)

Supplementary Table 2

Mean Number of Transcription Sites (with Standard Error of the Mean) per 100 Cells for each Diagnosis. (PDF 47 kb)

Supplementary Table 3

Diagnostic importance of gene expression profiling. (PDF 52 kb)

Supplementary Methods (PDF 84 kb)

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Capodieci, P., Donovan, M., Buchinsky, H. et al. Gene expression profiling in single cells within tissue. Nat Methods 2, 663–665 (2005) doi:10.1038/nmeth786

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