Computational Methods for Estimation of Cell Cycle Phase Distributions of Yeast Cells: Online Supplement

Citation: A. Niemistö, M. Nykter, T. Aho, H. Jalovaara, K. Marjanen, M. Ahdesmäki, P. Ruusuvuori, M. Tiainen, M.-L. Linne, and O. Yli-Harja, "Computational methods for estimation of cell cycle distributions of yeast cells".

Simulation of FACS measurements

In the original manuscript, we use simulated FACS data in the presentation of our method for estimating the distribution of a synchronized budding yeast cell population. The details of the simulation can be found in the supplementary PDF below.

Simulation of FACS measurements (PDF)

Time series budding yeast experiment

We have carried out an experiment in which alpha factor-based synchronization was used to synchronize a budding yeast cell population. The Saccharomyces cerevisiae strain Y01408 from Euroscarf (BY4741; MAT a; his3D1; leu2D0; met15D0; ura3D0; YIL015w::kanMX4) was used. In this time series experiment, samples of the cultivated population were imaged using a light microscope with the sampling interval of 2 minutes, and samples taken with the sampling interval of 6 minutes were analyzed with a FACS. The imaging and FACS analysis were performed for a total of 280 minutes.

The details of the experiment (PDF)

Image data

The images obtained in the experiment (ZIP, 43.9 Mb)

Each image corresponds to one sample (time instant) of the experiment. Each file has a name of the form sXXX_Y.jpg, where XXX is the running number of the sample and Y indicates multiple images (subsamples) taken of the same sample at the same time instant. For example, s024_1.jpg is one of the images taken at the time instant 48 minutes (the sampling interval is 2 minutes).

To make the size of the downloadable file reasonable, the images are in the JPEG format. The original TIFF images are available upon request (3.49 Gb total).

FACS data

The raw FACS data obtained in the experiment (ZIP, 9.4 Mb)

Each file in the raw FACS data corresponds to one sample (time instant) of the experiment. The first samples (28_10_02_001 - 28_10_02_006) were taken during alpha factor arrest (with a 15 minute sampling interval). The sample labeled 28_10_02_007 is the first sample taken after the release from synchronization. Each of the subsequent samples were then taken with a 6 minute sampling interval. The last sample was obtained 282 minutes after the first sample.

Each datafile includes data from 20000 cells (some data is missing in some datafiles). The data is stored in the standard FCS2.0 fileformat. Raw data can be read for example with the WinMDI software, or it can be read into MATLAB using the provided facsread.m function.

FACS histograms

The raw FACS histograms obtained in the experiment (PDF, 1.3 Mb)

Histograms were drawn from the raw FACS data measured during the experiment. Based on the histograms, the cell population seems to be at the G1 phase after the release from alpha factor arrest (time instants 0-14 minutes). A second peak appears (S phase) at 20-38 minutes. The majority of the cells has moved to the G2 phase when the second peak rises and the first peak disappears (68-98 minutes.) After this the first peak appears, and begins to rise again. However, the second peak does not disappear any more, indicating that the population starts to loose the synchrony.

Updated March 3, 2007