RNA-Seq of Sus scrofa: Porcine alveolar macrophages
RNA Sequencing and AnalysisPAM cells were seeded in a 12-well plate and divided into the following groups: D (DMSO), V (DMSO + SD16), A10V (A8-A2 10M + SD16), A20V (A8-A2 20M + SD16), and A30V (A8-A2 30M + SD16). After 24 hours, the cells were trypsinized, centrifuged, and washed twice with PBS. Trizol was added, and the samples were scraped into centrifuge tubes, which were then sent to Novogene Co., Ltd. The quality of the samples was assessed using the Agilent 2100 Bioanalyzer, total RNA was extracted, and transcriptome sequencing was performed on the Illumina sequencing platform. The sequencing data were processed using a pipeline that included fastp, HISAT2, StringTie, and featureCounts to generate the expression matrix. After normalization, differential expression analysis was conducted using the DESeq2(V1.20.0). The P-values were adjusted using the Benjamini and Hochberg method, and adjusted P-values  0.05 and |log2(fold change)|  1 were set as the thresholds for significant differential expression. GO and KEGG enrichment analyses of differentially expressed genes were performed using the clusterProfiler software (V3.8.1). Alternative splicing event analysis was conducted using the rMATS(V4.1.0).