Type 2 and interferon inflammation strongly regulate SARS-CoV-2 related gene expression in the airway epithelium

Satria P. Sajuthi; Peter DeFord; Nathan D. Jackson; Michael T. Montgomery; Jamie L. Everman; Cydney L. Rios; Elmar Pruesse; James D. Nolin; Elizabeth G. Plender; Michael E. Wechsler; Angel CY Mak; Celeste Eng; Sandra Salazar; Vivian Medina; Eric M. Wohlford; Scott Huntsman; Deborah A. Nickerson; Soren Germer; Michael C. Zody; Gonçalo Abecasis; Hyun Min Kang; Kenneth M. Rice; Rajesh Kumar; Sam Oh; Jose Rodriguez-Santana; Esteban G. Burchard; Max A. Seibold

In performing the CoV + and HRV + transcriptome-wide differential expression analyses, 738 to account for the class imbalance of this experiment, log 2 count-normalized expression 739 values in units of counts per million (calculated using edgeR v3.28.0) were passed to 740 the function arrayWeights function in the limma 55 R package (3.42.0). limma-voom was 741 then used to perform differential expression analysis on the count normalized 742 . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.09.034454 doi: bioRxiv preprint expression values between the CoV + and uninfected groups, as well as between the 743 HRV + and uninfected groups, controlling for age, gender, and asthma diagnosis status. 744