https://github.com/quantixed/p064p037

Code and data for manuscript p064p037
https://github.com/quantixed/p064p037

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Code and data for manuscript p064p037

• Host: GitHub
• URL: https://github.com/quantixed/p064p037
• Owner: quantixed
• License: gpl-3.0
• Created: 2023-10-27T13:30:58.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2025-02-24T08:42:07.000Z (12 months ago)
• Last Synced: 2025-02-24T09:32:06.541Z (12 months ago)
• Topics: paper
• Language: R
• Homepage:
• Size: 24.4 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# p064p037

[![DOI](https://zenodo.org/badge/710805399.svg)](https://doi.org/10.5281/zenodo.14916299)

Code and data for Fesenko et al. manuscript `#p064p037`

**ATG9A vesicles are a subtype of intracellular nanovesicle**

Mary Fesenko, Daniel J. Moore, Peyton Ewbank, Elizabeth Courthold & Stephen J. Royle

*bioRxiv* 2024. DOI: [https://doi.org/10.1101/2024.09.12.612637](https://doi.org/10.1101/2024.09.12.612637)

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# R code and data for recreation of plots

### Main Figures

- Volcano plots of WT, R159E, control `DM103104/Script/DM103104.R`

- Volcano plot of GFP-TPD54 knock-in INVs `proteomeAnalysis/Script/volcanoPlot.R`

- Combining data for analysis `DM103104/Script/upsetR.R`

- PANTHER/GO classification, TM analysis `proteomeAnalysis`

- TPD54 relocalization, ATG9A co-relocation `MF053`

- ATG9A relocalization, TPD54 co-relocation `MF046`

- Kinetics: ATG9A relocalization, TPD54 co-relocalization `MF041043`

	- Process data with `MF041043/Script/MF041043.R`

	- Load output into Igor with `MF041043/Script/MF041043.ipf`

	- Fit outputs from Igor are in `MF041043/Output/Data`

- ATG9 cargo co-relocalization `SJR234`

- LC3 western blot quantification `LC053`

- LC3 immunofluorescence quantification `MF122`

- ATG9 Golgi quantification `MF123`

### Supplementary Figures

- Comparison of WT, R159E, control `DM103104/Script/DM103104.R`

- Comparison of INV proteome with SLMV and ATG9 proteomes, Euler plots and replot of Judith et al. data to highlight INV proteins `ProteomicsComparison`

- ATG9A relocalization plot `MF046`

### Supplementary Tables

- Main INV proteome output for display is generated by `DM103104/Script/upsetR.R` - Supplementary Table 1

- INV proteome classification for display is generated by `proteomeAnalysis` - Supplementary Table 2

For cnvenience, both are available as Microsoft Excel files in `data/`