Analysis of gene expression by RNAseq
cough, tumor, fever
TUMOR, LUNG DISEASES, TUBERCULOSIS
Expression count matrices were retrieved from GEO: GSE147507-Series1 (Bronchial; culture), GSE153970 (Small airway; culture), GSE147507-Series15 (Autopsy), GSE145926- (Lavage). Differential gene expression analysis was performed using a Poisson-Tweedie distribution model using the tweeDEseq Bioconductor package (Bronchial culture samples are 3 independent primary normal human bronchial epithelial cultures infected apically with SARS-CoV-2 (USA-WA1/2020; MOI 2) for 24 hr, compared with three independent primary normal human bronchial epithelial Mock-infected with PBS for 24 hr.Small airway culture samples are three independent primary human airway epithelial cultures infected apically with SARS-CoV-2 (MOI 0.25) for 48 hr, compared with three independent primary human airway epithelial cultures Mock-infected with PBS for 48 hr.The autopsy samples are of two old (age >60) unidentified COVID-19 human subjects, who died due to COVID-19, had autopsy biopsy tissue acquisition post-mortem in Weill Cornell Medicine, and were provided as fixed samples for RNA extraction; the samples were compared with two old (age >60) unidentified human biopsy lung samples, taken during lung surgery and stored at Mount Sinai Institutional Biorepository and Molecular Pathology Shared Resource Facility (SRF) in the Department of Pathology, similarly provided as fixed samples for RNA extraction.COVID-19 patients’ lung epithelial cells are bronchoalveolar lavage fluid isolates from one severe case and five critical cases. The median age of the patients was 62.5 years, and the participants included four male and two female patients. All patients had Wuhan exposure history and had a cough and/or fever as the first symptom. Diagnosis of SARS-CoV-2 was based on clinical symptoms, exposure history, chest radiography and SARS-CoV-2 RNA-positive using commercial quantitative PCR with reverse transcription (qRT–PCR) assays. The samples were compared to three healthy donor controls. The median age was 24 years, and the participants included one female and three male patients. These donors were confirmed to be free of tuberculosis, tumor, and other lung diseases through CT imaging and other laboratory tests.