series2_GSE147507 : SARS-CoV-2 (USA-WA1/2020) viral gene expression from infected (MOI 0.2) A549 Cells

RNA-Seq reads (FASTQ) of biological triplicates from A549 cells infected with SARS-CoV-2 (USA-WA1/2020, MOI 0.2) (series2_GSE147507) were downloaded from NCBI SRA, and data analysis was performed using CLC Genomics workbench (CLC v20). The reads were first aligned to the human genome (hg38) with annotations (Ensemble v91), and then all unmapped reads were aligned to the SARS-Cov-2 reference genome NC_045512. The expression of each virus gene is quantified and reported as total counts and transcripts per million (TPM).<br>本研究从NCBI序列读取档案（Sequence Read Archive, SRA）下载了数据集series2_GSE147507中的数据：该数据为感染严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）毒株USA-WA1/2020（感染复数Multiplicity of Infection, MOI=0.2）的A549细胞的三次生物学重复样本的RNA测序读段（FASTQ格式），并采用CLC基因组工作台（CLC v20）完成数据分析。具体分析步骤如下：首先将测序读段比对至带有注释的人类基因组hg38（注释版本为Ensembl v91），随后将所有未比对上的读段比对至SARS-CoV-2参考基因组NC_045512；最后对每个病毒基因的表达量进行定量，结果以总计数（total counts）与每百万转录本数（transcripts per million, TPM）两种形式报告。