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Updated: May 8, 2026

Studying Muscle Transcriptional Dynamics at Single-molecule Scales in Drosophila
Published on: September 8, 2023
Allele-specific detection of single mRNA molecules in situ
Clinton H Hansen1, Alexander van Oudenaarden
1Harvard University Graduate Biophysics Program, Harvard Medical School, Boston, Massachusetts, USA.
Abstract:
We describe a method for fluorescence in situ identification of individual mRNA molecules, allowing quantitative and accurate measurement, in single cells, of allele-specific transcripts that differ by only a few nucleotides. By using a combination of allele-specific and non-allele-specific probe libraries, we achieve >95% detection accuracy. We investigate the allele-specific stochastic expression of Nanog, which encodes a pluripotency factor, in murine embryonic stem cells.

