RDI Calculator: An Analysis Tool to Assess RNA Distributions in Cells

Michael Stueland, Tianhong Wang, Hye Yoon Park, Stavroula Mili

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


Localization of RNAs to various subcellular destinations has emerged as a widely used mechanism that regulates a large proportion of transcripts in polarized cells. A number of methodologies have been developed that allow detection and imaging of RNAs at single-molecule resolution. However, methodologies to quantitatively describe RNA distributions are limited. Such approaches usually rely on the identification of cytoplasmic and nuclear boundaries which are used as reference points. Here, we describe an automated, interactive image analysis program that facilitates the accurate generation of cellular outlines from single cells and the subsequent calculation of metrics that quantify how a population of RNA molecules is distributed in the cell cytoplasm. We apply this analysis to mRNAs in mouse and human cells to demonstrate how these metrics can highlight differences in the distribution patterns of distinct RNA species. We further discuss considerations for the practical use of this tool. This program provides a way to facilitate and expedite the analysis of subcellular RNA localization for mechanistic and functional studies.

Original languageEnglish (US)
Article number8267
JournalScientific reports
Issue number1
StatePublished - Dec 1 2019
Externally publishedYes

Bibliographical note

Funding Information:
We thank all members of the Mili lab for useful discussions and suggestions. This work was supported by the Intramural Research Program of the Center for Cancer Research, NCI, National Institutes of Health (S.M.).

Publisher Copyright:
© 2019, The Author(s).


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