p053p030

Code and data for Ryan & Shelford et al. manuscript #p053p030

Defining endogenous TACC3–chTOG–clathrin–GTSE1 interactions at the mitotic spindle using induced relocalization

Ellis L Ryan^, James Shelford^, Teresa Massam-Wu, Richard Bayliss, Stephen J Royle

J. Cell Sci. (2021) 134(3): jcs255794 10.1242/jcs.255794

Data

• live_ksw contains the outputs from Fiji (knocksideways_spindle.ijm). Organised by cell line, these csv files can be used to generate ternary diagrams and arrow plots for live knocksideways experiments using SpindleQuantFromFiji.ipf.
• progression has mitotic progression data for all cell lines
• sequences directory contains the DNA sequences of the plasmids used introducing GFP-FKBP tags during gene editing.

Data for R plots are in the R directory.

Fiji Code

knocksideways_spindle.ijm will generate the data from a pre and post rapamycin image from a knocksideways experiment movie. Suggested data organisation: each movie has a directory with two images, run the code on this directory. These directories can be grouped by protein-of-interest and then by cell line (as described below.

Igor Code

• SpindleQuantFromFiji.ipf this code will read all the outputs from knocksideways_spindle.ijm. Data should be organised as follows: cell lines in separate directories, sub-directories for each protein assessed by live knocksideways. Consistent naming is required. Point Igor at the the directory which contains the cell line directories.
• MitoticProgression.ipf this code will read data from Excel workbooks. Data should be organised as follows: separate worksheets for the cells to be compared. Three columns per sheet labelled NEB, Metaphase, Anaphase. Each row is contains the frame number each cell reached these stages. Data used in the paper can be found in Data/progression

R Code

Three R projects to generate plots in the paper.

• fixed_ksw_figure
• gtse1_lidl_figure
• gtse1_fragment_figure

All work in a similar way. Data (outputs from Fiji) are in the Data directory and can be processed experiment-by-experiment or cell line by cell line to generate dataframes that are saved to Output/Data. A further script then calculates the statistics and plots the data.