Lipopolysaccharide (LPS) is a bacterial endotoxin which can participate in the induction of inflammatory responses. LPS may also play a significant role in some neurodegenerative, oncological and metabolic disorders. The aim of the current study was to determine the effect of a subclinical low single dose of LPS from Salmonella Enteritidis administrated in vivo on the transcriptome of porcine adrenal cortex cells, especially gene expression levels, long non-coding RNA (lncRNA) profiles, alternative splicing events and RNA editing sites using RNA-seq technology. The subclinical dose of LPS changed the expression of 354 genes, 27 lncRNA loci and other unclassified RNAs. An analysis of alternative splicing events revealed 104 genes with differentially expressed splice junction sites, and the single nucleotide variant calling approach supported the identification of 376 canonical RNA editing candidates and 7249 allele-specific expression variants. The obtained results suggest that the RIG-I-like receptor signaling pathway, may play a more important role than the Toll-like signaling pathway after the administration of a subclinical dose of LPS. Single subclinical dose of LPS can affect the expression profiles of genes coding peptide hormones, steroidogenic enzymes and transcriptional factors, and modulate the endocrine functions of the gland.