Title	Author
Type 2 and interferon inflammation strongly regulate SARS-CoV-2 related gene expression in the airway epithelium	Satria P. Sajuthi, Peter DeFord, _et al_

This repository contains scripts used to produce the figures within the paper "Type 2 and interferon inflammation strongly regulate SARS-CoV-2 related gene expression in the airway epithelium" (bioRxiv). They are organized as follow:

1. Nasal airway epithelium brushing bulk RNA-seq analysis.
2. Analysis of scRNA-seq data from the nasal epithelial brushing.
3. Analysis of bulk RNA-seq data from IL-13 and HRV infected ALI nasal airway epithelial cultures.
4. Analysis of scRNA-seq data from 10 day IL-13-stimulated and control tracheal cell ALI cultures.

The necessary packages to load can be found at the top of each script. We used R version 3.5.1 for all analyses.

Nasal airway epithelium brushing bulk RNA-seq analysis

• WGCNA.R - performs weighted gene coexpression network analysis on 695 RNA-seq samples
• T2_and_interferon_analysis.R
  • Association analyses between T2 related module eigengenes (MEpink and MEsaddlebrown) and expression of ACE and TMPRSS2 (Fig. 2b-g)
  • Association analyses between interferon related module eigengenes (MEtan and MEpurple) and expression of TMPRSS2 (Fig. 4a,b,d)
  • Hierarchical clustering based on the tan and saddlebrown modules genes (SFig. 1a, 2a)
• Multivariate_Regression_Analysis.R - performs multivariate regression analysis on the following models (Table 1):
  • ACE2 expr. ~ age + interferon_status + type2_status + sex + Asthma_Status + rs181603331
  • TMPRSS2 expr. ~ age + interferon_status + type2_status + sex + Asthma_Status + rs1475908 + rs74659079 + rs2838057
• inVivo_virus_Diff_Gene_Expression.R - Performs differential expression analysis between virus infected individuals and uninfected individuals for two sets of viruses:
  • Human coronaviruses
  • Pooled human rhinovirus C, Influenza A, Influenza B, Orthopneumovirus, Metapneumovirus, Enterovirus, and Parainfluenza.

Analysis of scRNA-seq data from the nasal epithelial brushing

• Nasal_brush_10X_analysis.R - carries out analyses on the nasal brushing 10X scRNA-seq data including clustering, UMAP visualization of cell populations (Fig 1a), find marker genes among cell populations, violin plots of ACE2 and TMPRSS2 (Fig. 1b-c)

Analysis of bulk RNA-seq data from IL-13 and HRV infected ALI nasal airway epithelial cultures

• HRV_IL13_ALI_analysis.R - carries out differential expression analyses between paired IL-13-stimulated and control samples (N = 5 donors, Fig. 3b,c) and between paired HRV-infected and control samples (N = 5 donors, Fig. 4g,h)

Analysis of scRNA-seq data from 10 day IL-13-stimulated and control tracheal cell ALI cultures

• IL-13_singleCell.R - carries out analyses on the tracheal 10X scRNA-seq data including clustering, UMAP visualization of cell populations (Fig 3d), find marker genes among cell populations, differential expression analysis between unstim. and IL-13 stimulated sample (Fig. 3e,f)