Cell Cycle Omics describes genome-scale protein concentration and localization dynamics during the yeast cell cycle based on protein-GFP fusions (Litsios et al. 2024). Cell cycle-resolution has been achieved via in silico synchronization of single cells expressing fluorescent cell cycle markers from static microscopy images. Cells were imaged using confocal microscopy, and proteome localization and concentration were quantified using DeepLoc, a deep convolutional neural network (CNN) for automated classification of proteins to different subcellular compartments (Kraus et al. 2017). Cell cycle-resolution was achieved using CycleNet, a newly developed CNN for in silico synchronization of single cells from microscopy images of unperturbed cell populations (Litsios et al. 2024). Each field of view was imaged in three channels: the green channel represents a GFP-fused protein from the ORF-GFP collection (Huh et al. 2003), while the red and far-red channels identify the nucleus and the cytoplasm and were used for cell segmentation purposes. The proteome data are complemented with population-level, cell cycle-resolved gene expression and translational efficiency data. Cell cycle-resolved gene expression and translational efficiency measurements were obtained at the population level using RNA sequencing (Couvillion and Churchman 2017) and Ribosome Profiling (Ingolia 2010), after synchronization of cells with the α-factor mating hormone (Breeden 1997). All omics datasets were scored using the same statistical metrics to identify proteins/transcripts with cell cycle-periodic regulation.
The Protein Concentration and Protein Localization Data section displays in the first row the concentration
of the specific protein, in arbitrary units, for five cell cycle phases (G1 Post-START, S/G2, Metaphase,
Anaphase, Telophase) and for two biological replicates.
Each of the following rows denotes the localization of the protein in the indicated localization class for
the respective cell cycle phases and biological replicates. The localization values denote DeepLoc
activation; DeepLoc produces for each cell cycle phase a vector representing the distribution over all
examined localization classes, with the values across all localization classes summing up to 1.
The Sequencing Data section displays the levels (RPKM, normalized reads per kilobase) and translational efficiency (ribosome profiling RPKM values divided by RNA-seq RPKM values) of the transcript of the queried gene, in the first and second rows, respectively, for five cell cycle phases (G1 Post-START, S/G2, Metaphase, Anaphase, Telophase) and for two biological replicates.
The Hit Data section indicates whether a gene was found to be periodic during the cell cycle in each of the indicated datasets.