/p054p031

Code and data for p054p031

Primary LanguageIGOR ProGNU General Public License v3.0GPL-3.0

p054p031

Code and data for Larocque et al. manuscript #p054p031

Intracellular nanovesicles mediate α5β1 integrin trafficking during cell migration

Gabrielle Larocque, Daniel J. Moore, Méghane Sittewelle, Cansu Kuey, Joseph H.R. Hetmanski, Penelope J. La-Borde, Beverley J. Wilson, Nicholas I. Clarke, Patrick T. Caswell and Stephen J. Royle

J Cell Biol, 220: e202009028 doi: 10.1083/jcb.202009028

Data

  • cell_migration cell track data in excel workbooks or directories of CSV files for analysis using CellMigration
  • cell_shape IMOD models and corresponding text files (produced by model2point) for analysis using CellShape
  • variance excel workbooks with spatiotemporal data for Rab GTPases and TPD54 mutants.

Data for R plots are in the R directory.

Scripts

  • ImageVariance.ipf a workflow to analyze cropped images for spatiotemporal variance in IgorPro
  • MakeEffectSizeGraph.ipf simple graphing procedure using R output of estimation statistics e.g. rabscreen_figure
  • MitoAggregation.ipf analysis of outputs from the Fiji script MitoAggregation.ijm which will extract statistics of mitochondria from cell limages
  • ProteomicsProcs.ipf a workflow used in conjunction with VolcanoPlot

R Code

Three R projects to generate plots in the paper.

  • cancer_figure - plotting data from TCGA
  • heatmap_figure - hierarchical clustering of Rab screen data
  • rabscreen_figure - calculating effect sizes from raw data

All work in a similar way. Data files are in the Data directory and are processed by an R script in Script to generate outputs that are saved to Output/Data or Output/Plots.