REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
RNA Seq Data	dbGAP	phs002258.v1.p1
	CRAN	V4.0.3 for Windows
Software and algorithms
Bash/PBS scripts for aligning data	All original code has been deposited at Github and is publicly available as of the date of	https://github.com/asaravia-butler/COV-IRT/blob/main/RNAseq/Raw_to_Aligned_Data_Pipeline.md.
R scripts for analysis	All original code is available in this paper’s supplemental information	https://github.com/rob-meller/iSCIENCE-COVIDpaper
R (v 4.0.3)		https://www.r-project.org/
HTStream		https://s4hts.github.io/HTStream/
STAR v	Dobin et al., 2013	https://github.com/alexdobin/STAR
Samtools v	Li et al., 2009	www.htslib.org
Picard Tools		https://broadinstitute.github.io/picard/
Limma	Ritchie et al. 2015	https://bioconductor.org/packages/release/bioc/html/limma.html
Enhanced volcano		(https://github.com/kevinblighe/EnhancedVolcano
TopGO		https://bioconductor.org/packages/release/bioc/html/topGO.html
FSGEA	Korotkevich et al. 2019	https://bioconductor.org/packages/release/bioc/html/fgsea.html
MuSIC	Wang et al. 2019	https://xuranw.github.io/MuSiC/articles/MuSiC.html