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Nat Protoc. 2013 Feb;8(2):282-301. doi: 10.1038/nprot.2012.158. Epub 2013 Jan 10.

Stochastic profiling of transcriptional regulatory heterogeneities in tissues, tumors and cultured cells.

Author information

1
Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA.

Abstract

Single-cell variations in gene and protein expression are important during development and disease. Such cell-to-cell heterogeneities can be directly inspected one cell at a time, but global methods are usually not sensitive enough to work with the starting material of a single cell. Here we provide a detailed protocol for stochastic profiling, a method that infers single-cell regulatory heterogeneities by repeatedly sampling small collections of cells selected at random. Repeated stochastic sampling is performed by laser-capture microdissection or limiting dilution, followed by careful exponential cDNA amplification, hybridization to microarrays and statistical analysis. Stochastic profiling surveys the transcriptome for programs that are heterogeneously regulated among cellular subpopulations in their native tissue context. The protocol is readily optimized for specific biological applications and takes about 1 week to complete.

PMID:
23306461
PMCID:
PMC3818581
DOI:
10.1038/nprot.2012.158
[Indexed for MEDLINE]
Free PMC Article

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