SARS-CoV-2 infection evokes transcriptional changes in Calu-3 cells and cultured primary mouse trigeminal ganglia cells

SARS-CoV-2, the virus responsible for COVID-19, infects both human airway epithelial cells and trigeminal ganglia. We assessed the consequences of SARS-CoV-2 infection on gene expression in Calu-3 cells and in primary Mus musculus trigeminal ganglia cells (mmTG). Here, we provide datasets that include raw reads and mapped reads for the following: 1) mock infected mmTG 48 hrs post infection; 2) SARS-CoV-2 infected mmTG 48 hrs post infection; 3) mock infected Calu-3 cells 24 hrs post infection; 4) SARS-CoV-2 infected Calu-3 cells 24 hrs post infection; 5) mock infected Calu-3 cells 48 hrs post infection; 6) SARS-CoV-2 infected Calu-3 cells 48 hrs post infection. Overall design: All mice were housed in standard conditions in accordance with standards approved by the Animal Care and Use Committee of the University of California Berkeley (14 hour light: 10 hour dark cycle, 21 °C). C57BL/6N mice were obtained from Charles River. Mouse trigeminal ganglia were cultured as previously described (Hill et al. 2018 J. Neurosci, PMID: 30082422; Wilson et al. 2011, Nature Neuro, PMID: 21460831) and plated in a 96-well plate. Eight trigeminal ganglia from 4 animals were combined and plated across 8 wells. TG cultures were infected with 500,000 SARS-CoV-2 (WA1) virions in medium (10% heat-inactivated FBS, sodium pyruvate, HEPES, L-glutamine, penicillin/streptomycin) or medium (mock infection) for 48 hours. Human adenocarcinoma lung epithelial (Calu-3) cells (ATCC, HTB-55) were maintained with RPMI (Fisher Scientific) supplemented with fetal bovine serum (FBS), L-glutamine, penicillin/streptomycin. Approximately 500,000 Calu-3 cells were incubated with SARS-CoV-2 (WA1) virions in medium (10% heat-inactivated FBS, sodium pyruvate, HEPES, L-glutamine, penicillin/streptomycin) diluted in phenol-red free RPMI to an MOI of 1 for 24 or 48 hours. After removing supernatant from infected cells, RNA was isolated with DNA/RNA Shield (Zymo Research) according to the manufacturer's instructions.