Hansen, Clintonvan Oudenaarden, Alexander2014-04-112013Hansen, Clinton H., and Alexander van Oudenaarden. 2013. “Allele-specific detection of single mRNA molecules in situ.” Nature methods 10 (9): 869-871. doi:10.1038/nmeth.2601. http://dx.doi.org/10.1038/nmeth.2601.1548-7091http://nrs.harvard.edu/urn-3:HUL.InstRepos:12064358We describe a method for fluorescent in situ identification of individual mRNA molecules, allowing quantitative and accurate measurements of allele-specific transcripts that differ by only a few nucleotides, in single cells. By using a combination of allele-specific and non-allele-specific probe libraries, we achieve over 95% detection accuracy. We investigate the allele-specific stochastic expression of the pluripotency factor Nanog in murine embryonic stem cells.en-USJournal Article2014-04-1110.1038/nmeth.2601