REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological Samples
Human bronchoalveolar lavage fluid samples	Peking University People’s Hospital, Shenzhen Third People’s Hospital, Fujian Provincial Hospital, the Second Affiliated Hospital of Harbin Medical University, the First Affiliated Hospital of Xi’an Jiaotong University, and hospitals in Wuhan	NA
Chemicals, Peptides, and Recombinant Proteins
Trizol LS	Thermo Fisher Scientific	Cat#10296028
Critical Commercial Assays
Direct-zol RNA Miniprep Kit	Zymo Research	Cat#R2051
Trio RNA-Seq Library Preparation Kit	NuGEN	Cat#0357-32
Deposited Data
Reads mapped to human genome GRCh38 extracted from the raw sequencing data	This paper	Genome Warehouse in National Genomics Data Center https://bigd.big.ac.cn/gsa; Project number: PRJCA002273
Software and Algorithms
HISAT2 v2.1.0	Kim et al., 2019	http://ccb.jhu.edu/software/hisat2/
FeatureCounts 2.0.0	Liao et al., 2014	http://subread.sourceforge.net/
Fastp 0.20.0	Chen et al., 2018	https://github.com/OpenGene/fastp
Quantile normalization (Bioconductor limma package v3.42.2)	Ritchie et al., 2015	https://www.bioconductor.org/packages/release/bioc/html/limma.html
Ingenuity Pathway Analysis, December 2019 release (v499329)	Krämer et al., 2014	https://digitalinsights.qiagen.com/
Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis (Bioconductor clusterProfiler package v3.14.3)	Yu et al., 2012	https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html
STRING v11	Szklarczyk et al., 2019	https://string-db.org
Cytoscape v3.7.1	Shannon et al., 2003	https://cytoscape.org
CIBERSORT algorithm v1.06	Newman et al., 2015	https://cibersort.stanford.edu/
Samtools 1.9	Li et al., 2009	http://samtools.sourceforge.net/