Bulk RNA-seq of Hamster Lung Tissue

Right lung caudal lobe was harvested from the animals and homogenized in trizol. RNA purification was performed with the kit RiboPure^™ RNA Purification Kit following manufacturer’s instructions. Sequencing libraries were generated with the Illumina Total RNA Prep with Ribo-Zero Plus kit. These libraries were sequenced on an Illumina NovaSeq 6000 using an S4 flow cell, generating paired-end 100 bp reads. Adapter sequences were trimmed from reads with Cutadapt^{75 (link)}, then pseudoaligned by Kallisto^{76 (link)} to the Golden Hamster transcriptome. The transcriptome index was built from the MesAur1.0 genome assembly and gene annotation from Ensembl release 100. Differentially expressed genes were identified using DESeq2^{77 (link)}. Cell types were deconvoluted from bulk RNA-seq profiles with CIBERSORTx^{78 (link)}. A signature matrix was built from a single-cell Golden Hamster lung dataset^{31 (link)}, which was randomly down-sampled to 100 cells of each type. Cell fractions were imputed using default parameters and a normalized count matrix as input. Analysis were performed and graphs were performed in R, using the packages “DESeq2” (v 1.38.3), “pheatmap” (v 1.0.12) and “patchwork” (v 1.1.2).