Author: Michael Jay Corley; Christopher Sugai; Michael Schotsaert; Robert E. Schwartz; Lishomwa C Ndhlovu
Title: Comparative in vitro transcriptomic analyses of COVID-19 candidate therapy hydroxychloroquine suggest limited immunomodulatory evidence of SARS-CoV-2 host response genes. Document date: 2020_4_14
ID: 30x26ip7_49
Snippet: Reads were aligned with STAR[35] 2.7.3a in two-pass quantification mode. A custom reference was generated comprising Ensembl GrCh38 release 98 and SARS-CoV-2 2019-nCoV/USA-WA1/2020 (NCBI Nucleotide MN985325.1) to detect viral RNA. Tabulated counts were checked for expected stranded-ness and concatenated in R. Normalization, gene filtering, and differential expression analysis was done edgeR [7] . Genes were filtered for a minimum read count above.....
Document: Reads were aligned with STAR[35] 2.7.3a in two-pass quantification mode. A custom reference was generated comprising Ensembl GrCh38 release 98 and SARS-CoV-2 2019-nCoV/USA-WA1/2020 (NCBI Nucleotide MN985325.1) to detect viral RNA. Tabulated counts were checked for expected stranded-ness and concatenated in R. Normalization, gene filtering, and differential expression analysis was done edgeR [7] . Genes were filtered for a minimum read count above 10 and log fold change greater than 1. Counts were annotated with AnnotationHub.
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