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本数据集包含用于复现论文中所有统计分析与图表的数据与代码。报告的汇总输出结果已存储于文件`organoids.docx`与`nc.docx`中。 `code.zip` 压缩包内含源代码。其中，`organoids.qmd` 用于复现类器官分析流程，`nc.qmd` 则用于复现人类鼻上皮细胞的相关分析。其余文件为辅助文件，保障主分析流程正常运行。 本分析基于R语言与Quarto工具完成。 研究采用renv包以复现完整的计算运行环境。 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`：本次测量所用培养板的孔位编号 `time`：测量开始后的时长 `area`：类器官的面积 `patient`：患者的匿名编号 `date`：实验开展日期（日期与患者编号可唯一标识一块培养板） `filename`：该培养板对应的原始数据存储文件名（未公开），可唯一标识一块培养板 `mix`：标识所用的两种培养板布局之一 `replicate`：技术重复编号（同一块培养板上的每个条件均设置2次技术重复） `type`：实验主条件，可选值包括："VTI"（Vanzacator + Tezacaftor + Ivacaftor）、"VTI_2"、"VTI_02"、"VTI_002"（与VTI配方一致，但Vanzacaftor浓度分别为2、0.2、0.02 μM）、"ETI"（Elaxacaftor + Tezacaftor + Ivacaftor）、"FskOnly"（仅使用福司柯林的对照组） `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`：细胞预处理方式，可选值包括："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`：实验开始时的跨膜电阻（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ID