Code and data for the manuscript "Tidal ventilation induces divergent repair responses in lung epithelial cells and fibroblasts mediated by IL-6 signalling" The folder contains the following files:
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"Lung_repair.R": R script used to load and process all the data files described below. All the analyses and figures shown in the manuscript are generated with this script.
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"Wound_healing_BEAS.xlsx": Sheet 1. Raw data used to quantify the wound healing assay in BEAS-2B cells supplemented with BALF from MV or CPAP patients.
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"Samples_BEAS": Sheet 1. Contains ColData (sample metadata) used for BEAS-2B RNA-seq analysis.
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"transcripts_BEAS_github.rds": Count matrix from BEAS-2B RNA-seq samples supplemented with BALF from MV or CPAP patients. STRING protein-protein interaction network was downloaded from the STRING website: https://version-11-5.string-db.org/cgi/download?sessionId=b4uePWoT3fVG
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"Wound_healing_MRC5.xlsx": Sheet 1. Raw data used to quantify the wound healing assay in MRC5 cells supplemented with BALF from MV or CPAP patients.
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"Samples_MRC5": Sheet 1. Contains ColData (sample metadata) used for MRC5 RNA-seq analysis.
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"transcripts_MRC5_github.rds": Count matrix from MRC5 RNA-seq samples supplemented with BALF from MV or CPAP patients. STRING protein-protein interaction network was downloaded from the STRING website: https://version-11-5.string-db.org/cgi/download?sessionId=b4uePWoT3fVG
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"Wound_healing_BEAS.xlsx": Sheet 2. Raw data used to quantify the wound healing assay in BEAS-2B cells with BALF from MV or CPAP patients treated with tocilizumab.
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"Samples_BEAS": Sheet 2. Contains ColData (sample metadata) used for BEAS-2B with tocilizumab RNA-seq analysis.
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"transcripts_BEAS_toci_github.rds": Count matrix from BEAS-2B RNA-seq samples supplemented with BALF from MV or CPAP patients treated with tocilizumab.
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"Wound_healing_MRC5.xlsx": Sheet 2. Raw data used to quantify the wound healing assay in MRC5 cells with BALF from MV or CPAP patients treated with tocilizumab.
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"Samples_MRC5": Sheet 2. Contains ColData (sample metadata) used for MRC5 with tocilizumab RNA-seq analysis.
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"transcripts_MRC5_toci_github.rds": Count matrix from MRC5 RNA-seq samples supplemented with BALF from MV or CPAP patients treated with tocilizumab.
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"protein_abundance_github.rds": Protein abundance matrix obtained from BALF proteomic analysis from patients under MV or CPAP.
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"human_lr_pair.rds": Database of human ligand–receptor pairs from CellTalkDB. STRING protein-protein interaction network was downloaded from the STRING website: https://version-11-5.string-db.org/cgi/download?sessionId=b4uePWoT3fVG
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"transcripts_interaction_analysis_github.rds": Count matrix from BEAS-2B RNA-seq samples supplemented with BALF from MV or CPAP patients not treated and treated with tocilizumab used for interaction analysis.
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"qPCR_BEAS_CsA": Raw qPCR data from IL-6 and PPIA relative expression in BEAS-2B cell line supplemented with BALF from MV or CPAP patients treated with cyclosporine-A (CsA).
Note: The string data is loaded in the code using: <- read.table("9606.protein.links.v11.5.txt", header = T)"
CONTACT Laura Amado Rodríguez (lar@crit-lab.org / laura.amado@sespa.es)