An automated workflow for quantifying RNA transcripts in individual cells in large data-sets.

ABSTRACT: Advanced molecular probing techniques such as single molecule fluorescence in situ hybridization (smFISH) or RNAscope can be used to assess the quantity and spatial location of mRNA transcripts within cells. Quantifying mRNA expression in large image sets usually involves automated counting of fluorescent spots. Though conventional spot counting algorithms may suffice, they often lack high-throughput capacity and accuracy in cases of crowded signal or excessive noise. Automatic identification of cells and processing of many images is still a challenge. We have developed a method to perform automatic cell boundary identification while providing quantitative data about mRNA transcript levels across many images. Comparisons of mRNA transcript levels identified by the method highly correlate t

SUBMITTER: Pharris MC 

PROVIDER: S-EPMC5596354 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature