Abstract
Two computational methods for estimating the cell cycle phase distribution of a budding yeast (Saccharomyces cerevisiae) cell population are presented. The first one is a nonparametric method that is based on the analysis of DNA content in the individual cells of the population. The DNA content is measured with a fluorescence-activated cell sorter (FACS). The second method is based on budding index analysis. An automated image analysis method is presented for the task of detecting the cells and buds. The proposed methods can be used to obtain quantitative information on the cell cycle phase distribution of a budding yeast S. cerevisiae population. They therefore provide a solid basis for obtaining the complementary information needed in deconvolution of gene expression data. As a case study, both methods are tested with data that were obtained in a time series experiment with S. cerevisiae. The details of the time series experiment as well as the image and FACS data obtained in the experiment can be found in the online additional material at http://www.cs.tut.fi/sgn/csb/yeastdistrib/http://www.cs.tut.fi/sgn/csb/yeastdistrib/.
Highlights
Many recent studies have concentrated on the construction of dynamic models for genetic regulatory networks [1,2,3,4]
The first one is a nonparametric method that is based on the analysis of DNA content in the individual cells of the population
The DNA content is measured with a fluorescence-activated cell sorter (FACS)
Summary
Many recent studies have concentrated on the construction of dynamic models for genetic regulatory networks [1,2,3,4]. In earlier studies with budding yeast [5, 7, 8], an estimate for the cell cycle phase distribution of a cell population has been. Cells that are in the G1 phase are assumed not to have a bud, cells that are in the S phase are assumed to have a small bud, and cells that are in the G2/M phase are assumed to have a large bud Based on these assumptions, we propose two computational high-throughput methods for estimating the cell cycle phase distribution of a budding yeast cell population. The estimate of the time distribution is obtained by performing budding index analysis through image analysis.
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