{"id":19998759,"url":"https://github.com/quantixed/p065p038","last_synced_at":"2025-07-04T23:40:17.648Z","repository":{"id":242108223,"uuid":"765366411","full_name":"quantixed/p065p038","owner":"quantixed","description":"Data and code for p065p038","archived":false,"fork":false,"pushed_at":"2024-10-30T08:09:41.000Z","size":8570,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-12T12:45:28.390Z","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":"2024-02-29T19:28:56.000Z","updated_at":"2024-10-30T08:09:45.000Z","dependencies_parsed_at":null,"dependency_job_id":"8ce3ac1f-c962-47ff-a963-49179a280b3c","html_url":"https://github.com/quantixed/p065p038","commit_stats":null,"previous_names":["quantixed/p065p038"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2Fp065p038","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2Fp065p038/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2Fp065p038/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2Fp065p038/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/quantixed","download_url":"https://codeload.github.com/quantixed/p065p038/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":"2024-11-13T05:09:24.862Z","updated_at":"2025-07-04T23:40:17.642Z","avatar_url":"https://github.com/quantixed.png","language":"R","readme":"# p065p038\n\nCode and data for Downie et al. manuscript `#p065p038`\n\n**Non-disruptive inducible labeling of ER-membrane contact sites using the Lamin B Receptor**\n\nLaura Downie, Nuria Ferrandiz, Elizabeth Courthold, Megan Jones, \u0026 Stephen J. Royle\n\nPreprint: *bioRxiv* 2024. DOI: [https://doi.org/10.1101/2024.05.31.596797](https://doi.org/10.1101/2024.05.31.596797)\n\n--\n\n# R Code and data for recreation of plots\n\n### Main Figures\n\n- **Fig 1D,E,G** LBR cluster analysis (plasma membrane, 3D) - `SJR233` analysis of LD317\n- **Fig 1I** LBR cluster analysis (plasma membrane, 2D movie) - `SJR217` analysis of LD295\n- **Fig 2B,C** MAPPER + LBR cluster analysis - `SJR239` analysis of LD347 (6 repeats)\n- **Fig 3C** Individual line profiles with image outputs - `SJR248`\n- **Fig 3D** Line profile comparison - `SJR266` analysis of LD237, LD239, LD352, LD365, LD360\n- **Fig 4C,D** Mitochondria-ER contact analysis from SBF-SEM - `SJR242`\n- **Fig 5B** Line profile comparison - `SJR266` analysis of LD237, LD239, LD352, LD365, LD360\n- **Fig 7B** Golgi coloc - `SJR267` analysis of LD376\n\n### Supplementary Figures\n\n- **Fig S2B** Flow cytometry - `NF229`\n- **Fig S5B** Thapsigargin experiment - `SJR265` analysis of LD446\n- **Fig S6B** Line profile comparison (cell lines) - `profile_CellType`\n- **Fig S8B-D** LBR cluster sizes after 2h or 4h (3D) - `LBR_LongTerm`\n- **Fig S9** Individual line profiles with image outputs - `SJR248`\n- **Fig S11** Line profile comparison (constructs) - `profile_Regions`\n- **Fig S12D** ER expression of FKBP-GFP-tagged constructs under different promoters - `ERExpr`\n- **Fig S12E,F** Sec61 and LBR cluster analysis (3D) under different promoters - `Sec61Expr`\n\n\n### Notes\n\n- The R code can be executed with data placed into the `Data` folder of each RProject.\n- For RProject folders where data is absent from the `Data` folder, it is available seprately at zenodo ([10.5281/zenodo.15263507](https://doi.org/10.5281/zenodo.15263507)), due to GitHub space constraints. Download the data, add it to the `Data` folder and the analysis can proceed.\n- Fiji scripts for image analysis are included in the `Script` folder of each RProject.\n- Plots used in the paper can be found in `Output/Plots` or regenerated using the scripts provided.\n- The values plotted in each Figure are exported to `Output/Data` \n- For convenience, all of these files are collated in `plot_data_files`\n\n**The folder `plot_data_files` contains the numerical data underlying all plots in the manuscript.**\n\n\n### Additional data\n\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15263507.svg)](https://doi.org/10.5281/zenodo.15263507)\n\n### Archived version of the code\n\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15582238.svg)](https://doi.org/10.5281/zenodo.15582238)","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantixed%2Fp065p038","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fquantixed%2Fp065p038","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantixed%2Fp065p038/lists"}