RNA-Seq of SARS-CoV-2 infected Calu-3 cells
Calu-3 cells were obtained from ATCC (HTB-55) and cultured in EMEM (ATCC 30-2003) supplemented with 10% heat-inactivated FBS (Hyclone, SH30396.03) following ATCCs method.    SARS-CoV-2 USA-WA1/2020 (Gen Bank: MN985325.1) was obtained from BEI Resources and expanded and tittered on Vero cells. Cells were infected in DMEM +2% FBS.    RNA extraction was done with RNeasy Plus Micro Kit (Qiagen 74034) following manufacturers protocol.    Libraries were constructed with the KAPA mRNA HyperPrep kit (Roche 08098115702).     The libraries were loaded onto an HiSeq 2500 (Illumina) and sequenced for 120 cycles from one end of the fragments.    Basecalls were performed using Illumina offline basecaller (OLB) and then demultiplexed.