Effect of vanzacaftor on cystic fibrosis airway epithelial cells compared to elexacaftor - Data and statistical analysis

Data and code to reproduce all statistical analyses and figures in the manuscript. Compiled outputs from the reports are available in files "organoids.docx" and "nc.docx". The `code.zip` archive contains the source code. The file "organoids.qmd" reproduces the organoid analyses, file "nc.qmd" reproduces the analysis for human nasal epithelial cells. Other files are supporting to let the main analysis run. The analysis is written in R + Quarto. The renv package is used for recreate the computational environment. The patient-derived organoids dataset is stored in the file `organoids_data.csv`, the columns are: `well` The ID of the well within the plate the measurement was taken `time` time from start of measurement `area` area of the organoids `patient` Anonymized ID of the patient `date` Date when the experiment was performed (date and patient ID identify the plate) `filename` The filename in raw data (not published) this plate was stored in. (uniquely identifies a plate) `mix` Identifies one od two variants of plate layouts used `replicate` ID of technical replicate (two technical replicates were done for each condition on the same plate) `type` The main condition - one of "VTI" (Vanzacator + Tezacaftor+Ivacaftor), "VTI_2", "VTI_02", "VTI_002" (same as VTI, but differing concentrations of Vanzacaftor - 2, 0.2 and 0.02 μM) "ETI" (Elaxacaftor + Tezacaftor+Ivacaftor", "FskOnly" (Control, only forskolin) `fsk_concentration` concentration of forskolin (μM) The human nasal epithelial cells dataset is stored in the file `nc_data.csv` the columns are: `id` anonymized ID of the patient `pretreatment` how the cells were treated - values: "Untreated", "ETI" (Elaxacaftor + Tezacaftor+Ivacaftor", "VTI" (Vanzacator + Tezacaftor+Ivacaftor), "Healthy_Ind0" - "Healthy_Ind50" (cells from healthy donors, treated with varying concentrations of indomethacin) `rt_start` resistance at start of experiment (Ω*cm2) `basal`,`ami`,`fsk_max_peak`,`fsk_final`,`vx770`,`inh172`,`atp` Isc values at individual time points (μA/cm2) `repl_id` unique ID for each row本数据集包含复现论文中所有统计分析与图表所需的全部代码与原始数据。报告的编译结果已保存至`organoids.docx`与`nc.docx`文件中。 `code.zip`归档文件包含完整源代码。其中`organoids.qmd`用于复现类器官分析流程，`nc.qmd`用于复现人类鼻上皮细胞的分析流程，其余文件为辅助运行主分析的配套脚本。 本分析基于R语言与Quarto（夸托）开发。 本项目使用`renv`包复现完整计算环境。 患者来源类器官数据集存储于`organoids_data.csv`文件中，各字段说明如下： - `well`：实验孔板中对应测量孔的唯一标识 - `time`：自测量启动起的时长 - `area`：类器官的面积 - `patient`：患者的匿名编号 - `date`：实验开展日期（结合患者ID可唯一标识一块孔板） - `filename`：该孔板对应的未公开原始数据存储文件名，可唯一标识一块孔板 - `mix`：孔板布局两种变体之一的标识 - `replicate`：技术重复编号（同一块孔板上的每个条件均设置2个技术重复） - `type`：核心处理条件，取值包括："VTI"（Vanzacator + Tezacaftor+Ivacaftor）、"VTI_2"、"VTI_02"、"VTI_002"（与VTI处理方案一致，仅Vanzacaftor浓度分别为2、0.2、0.02 μM）、"ETI"（Elaxacaftor + Tezacaftor+Ivacaftor）、"FskOnly"（对照组，仅添加福司柯林（forskolin）） - `fsk_concentration`：福司柯林的浓度（单位：μM） 人类鼻上皮细胞数据集存储于`nc_data.csv`文件中，各字段说明如下： - `id`：患者的匿名编号 - `pretreatment`：细胞预处理方案，取值包括："Untreated"（未处理）、"ETI"（Elaxacaftor + Tezacaftor+Ivacaftor）、"VTI"（Vanzacator + Tezacaftor+Ivacaftor）、"Healthy_Ind0"至"Healthy_Ind50"（来自健康供体的细胞，经不同浓度吲哚美辛处理） - `rt_start`：实验起始时的电阻值（单位：Ω·cm²） - `basal`、`ami`、`fsk_max_peak`、`fsk_final`、`vx770`、`inh172`、`atp`：各时间点的短路电流（Isc）值（单位：μA/cm²） - `repl_id`：每行数据的唯一标识