RNA from the lungs of control and experimental mice were sent for bulk sequencing separately. Approximately 0.4 µg of total RNA was used for library preparation. mRNA enrichment and library preparation were performed using the Polyadenylated (PolyA+) mRNA Magnetic Isolation Module (New England Biolabs) and NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), following the manufacturer’s protocol. All 12 samples were then pooled together and sequenced in one lane using Illumina Novaseq 6000 platform with paired-end 150 bp (Supplementary file 1a). The raw fastq files from RNA-seq were mapped to GRCm38 mouse genome reference using STAR (version 2.5) with default parameters. More than 90% (Supplementary file 1a) of sequenced paired-end reads (above 50M reads for each library) were mapped to the mouse genome by STAR (Dobin et al., 2013; RRID:SCR_015899). HTSeq (Anders et al., 2015; RRID:SCR_005514) (version 0.6.0) was used to quantify gene expression, with Ensembl GRCm38.96 as a reference. DESeq2 (RRID:SCR_015687; version 1.24.0) was used to perform the differential expression analysis on the HTSeq quantified count per gene. The top 200 up- and downregulated genes (Supplementary file 1b), ranked by p-value from low to high with fold change above 1.5 (or log2[fold change] > 0.58), were used for biological process enrichment analysis in the DAVID database. Biological process terms with at least five differentially expressed genes and BHQ < 0.15 were selected. For aggregating redundant biological processes, GOSemSim (Yu et al., 2010) (version 2.10.0) was used to calculate the semantic similarity (‘Jiang’ method from GOSemSim) between significant biological processes. Redundant biological processes were manually merged into biological process categories (Supplementary file 1c).

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