What do we do? Yeast ORF-GFP fusion library  4156 strains Synthetic promoters library  200 strains Cycling through the chamber array to aquire brightfield.

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What do we do? Yeast ORF-GFP fusion library  4156 strains Synthetic promoters library  200 strains Cycling through the chamber array to aquire brightfield and fluorescence images 1.5s. / chamber  20 min / 1152 strains 5D data Temporal resolution  Dynamic changes Spatial resolution  Localization Genomic resolution  70% of yeast genome

Overview Movie list Queries Single movie infoMultiple Movie info Database

Data structure Project 1 – YGFP dynamicsProject 2 – Synthetic promoters Experiment 1 Eg: /TL_ Movie 1 Eg: /pos1_L BF images *.tif Bulk data yORF_foldInduction.txt yORF_timeCourse.txt Manual annotation manualAnnotation.txt Fluo Images *.tif Movie info expData.txt Strain info YGFP_libInfo.txt Other ?  Row, Colum, Time stamp, ORF ID  ORF ID, Gene name, UCSF localization, FACS data, mRNA data, GO annotation ?  Quality check, Intensity changes, Localization changes, Comments  Main intensity, Localization changes  Simulation parameters, Segmentation/tracking info (cell label, outline, track, …), Single cell data (Intensity, Localization, Area, …) Description experimentInfo.txt Single-cell info Eg: /Pos1_L/out.xml

Queries Project Experiment Gene name, ORF ID Position within the chip (row, column) Intensity, Fold change (manual, bulk or single-cell data) Localization, Localization Changes (manual, bulk or single-cell data) UCSF localization Microarray data FACS data GO annotation Unique gene option? Which one to pick? Rating? Output: -List of genes / ORF ID -Tick selection -Display options -1 choice  movie, single cell data -n choices  overlay graphs -Export options

Display a single movie Fluo movieBF movie Choose analysis -Analysis 1 -Analysis 2, … Display options - Cell outline, label - Single-cell track - Select single cell and highlight the trace in the graphs Graph #1 - Cells intensity over time - Cells area over time - Localization over time - correlation plots (feat.1 vs feat.2)  Distribution, single traces, … Graph #2  Same options as Graph #1 Movie facts - Gene Name - GO - … Export Graphs  png, eps Export source data for editing in Matlab / R

Tracker display – An example

Display multiple movies Graph #1 - Mean intensity over time - Cells area over time - Localization over time - correlation plots (feat.1 vs feat.2)  Dendogram (clustering), Traces overlay Graph #2  Same options as Graph #1 Table (Changeable column) CheckORF IDgene nameMA – quality checkMA - commentsGO processGO function Options - Check/uncheck to modify the graphs below - Export new selection/table Export Graphs  png, eps Export source data for editing in Matlab / R

Database available to the public  Limited number of functionality – Queries by gene names, … (no experiment structure) – Acces to the raw images and download – Acces to the data and export – Display tools