Computational protocol: The histone deacetylase Hos2 forms an Hsp42-dependent cytoplasmic granule in quiescent yeast cells

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Protocol publication

[…] Unless otherwise specified, images are maximal projections of Z-stacks. However, for quantification of signal intensities, sum projections of Z-stacks were used. Intensity was measured using ImageJ (http://rsbweb.nih.gov/ij), and the background intensity was subtracted. When counting the number of protein foci, we examined at least 100 cells from three independent experiments by inspecting Z-sections of each cell and further confirmed using three-dimensional projections. To analyze and quantify the intensities and spatial distributions of GFP and mCherry signals, we used ImageJ and the three-dimensional graph function of softWoRx 3.7.1. For quantifying colocalization, we used JACoP () as a plug-in for ImageJ. Cell Counter (http://rsbweb.nih.gov/ij/plugins/cell-counter.html) was also used as a plug-in for ImageJ to count and categorize assemblies and cells. […]

Pipeline specifications

Software tools ImageJ, JACoP
Application Microscopic phenotype analysis
Organisms Saccharomyces cerevisiae
Chemicals Glucose