{"id":19998765,"url":"https://github.com/quantixed/p064p037","last_synced_at":"2025-03-01T23:28:35.211Z","repository":{"id":256792942,"uuid":"710805399","full_name":"quantixed/p064p037","owner":"quantixed","description":"Code and data for manuscript p064p037","archived":false,"fork":false,"pushed_at":"2025-02-24T08:42:07.000Z","size":25635,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-02-24T09:32:06.541Z","etag":null,"topics":["paper"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/quantixed.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-10-27T13:30:58.000Z","updated_at":"2025-02-24T08:42:11.000Z","dependencies_parsed_at":"2025-01-10T15:50:21.331Z","dependency_job_id":null,"html_url":"https://github.com/quantixed/p064p037","commit_stats":null,"previous_names":["quantixed/p064p037"],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2Fp064p037","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2Fp064p037/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2Fp064p037/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2Fp064p037/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/quantixed","download_url":"https://codeload.github.com/quantixed/p064p037/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241439486,"owners_count":19963095,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["paper"],"created_at":"2024-11-13T05:09:25.920Z","updated_at":"2025-03-01T23:28:35.206Z","avatar_url":"https://github.com/quantixed.png","language":"R","readme":"# p064p037\n\n[![DOI](https://zenodo.org/badge/710805399.svg)](https://doi.org/10.5281/zenodo.14916299)\n\nCode and data for Fesenko et al. manuscript `#p064p037`\n\n**ATG9A vesicles are a subtype of intracellular nanovesicle**\n\nMary Fesenko, Daniel J. Moore, Peyton Ewbank, Elizabeth Courthold \u0026 Stephen J. Royle\n\n*bioRxiv* 2024. DOI: [https://doi.org/10.1101/2024.09.12.612637](https://doi.org/10.1101/2024.09.12.612637)\n\n--\n\n# R code and data for recreation of plots\n\n### Main Figures\n\n- Volcano plots of WT, R159E, control `DM103104/Script/DM103104.R`\n- Volcano plot of GFP-TPD54 knock-in INVs `proteomeAnalysis/Script/volcanoPlot.R`\n- Combining data for analysis `DM103104/Script/upsetR.R`\n- PANTHER/GO classification, TM analysis `proteomeAnalysis`\n- TPD54 relocalization, ATG9A co-relocation `MF053`\n- ATG9A relocalization, TPD54 co-relocation `MF046`\n- Kinetics: ATG9A relocalization, TPD54 co-relocalization `MF041043`\n\t- Process data with `MF041043/Script/MF041043.R`\n\t- Load output into Igor with `MF041043/Script/MF041043.ipf`\n\t- Fit outputs from Igor are in `MF041043/Output/Data`\n- ATG9 cargo co-relocalization `SJR234`\n- LC3 western blot quantification `LC053`\n- LC3 immunofluorescence quantification `MF122`\n- ATG9 Golgi quantification `MF123`\n\n### Supplementary Figures\n\n- Comparison of WT, R159E, control `DM103104/Script/DM103104.R`\n- Comparison of INV proteome with SLMV and ATG9 proteomes, Euler plots and replot of Judith et al. data to highlight INV proteins `ProteomicsComparison`\n- ATG9A relocalization plot `MF046`\n\n### Supplementary Tables\n\n- Main INV proteome output for display is generated by `DM103104/Script/upsetR.R` - Supplementary Table 1\n- INV proteome classification for display is generated by `proteomeAnalysis` - Supplementary Table 2\n\nFor cnvenience, both are available as Microsoft Excel files in `data/`","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantixed%2Fp064p037","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fquantixed%2Fp064p037","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantixed%2Fp064p037/lists"}