Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Stueland M

PROVIDER: S-EPMC6547641 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Stueland Michael M Wang Tianhong T Park Hye Yoon HY Mili Stavroula S

Scientific reports 20190604 1

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 de ...[more]

PMID: 31164708

Similar Datasets

Project description:BackgroundDNA double-strand breaks can be counted as discrete foci by imaging techniques. In personalized medicine and pharmacology, the analysis of counting data is relevant for numerous applications, e.g., for cancer and aging research and the evaluation of drug efficacy. By default, it is assumed to follow the Poisson distribution. This assumption, however, may lead to biased results and faulty conclusions in datasets with excess zero values (zero-inflation), a variance larger than the mean (overdispersion), or both. In such cases, the assumption of a Poisson distribution would skew the estimation of mean and variance, and other models like the negative binomial (NB), zero-inflated Poisson or zero-inflated NB distributions should be employed. The model chosen has an influence on the parameter estimation (mean value and confidence interval). Yet the choice of the suitable distribution model is not trivial.MethodsTo support, simplify and objectify this process, we have developed the countfitteR software as an R package. We used a Bayesian approach for distribution model selection and the shiny web application framework for interactive data analysis.ResultsWe show the application of our software based on examples of DNA double-strand break count data from phenotypic imaging by multiplex fluorescence microscopy. In analyzing numerous datasets of molecular pharmacological markers (phosphorylated histone H2AX and p53 binding protein), countfitteR demonstrated an equal or superior statistical performance compared to the usually employed two-step procedure, with an overall power of up to 98%. In addition, it still gave information in cases with no result at all from the two-step procedure. In our data sample we found that the NB distribution was the most frequent, with the Poisson distribution taking second place.ConclusionscountfitteR can perform an automated distribution model selection and thus support the data analysis and lead to objective statistically verifiable estimated values. Originally designed for the analysis of foci in biomedical image data, countfitteR can be used in a variety of areas where non-Poisson distributed counting data is prevalent.

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets