RNA sequencing differential gene expression analysis of isolated perfused bovine udders experimentally inoculated with Streptococcus agalactiae

摘要

The aim of this study was to elucidate the differentialgene expression in the RNA sequencing transcriptomeof isolated perfused udders collected from 4 slaughteredHolstein × Zebu crossbred dairy cows experimentallyinoculated with Streptococcus agalactiae. We studied3 different statistical tools (edgeR, baySeq, and Cuffdiff2). In summary, 2 quarters of each udder wereexperimentally inoculated with Strep. agalactiae andthe other 2 were used as a control. Mammary tissuebiopsies were collected at times 0 and 3 h after infection.The total RNA was extracted and sequenced onan Illumina HiSeq 2000 (Illumina Inc., San Diego, CA).Transcripts were assembled from the reads aligned tothe bovine UMD 3.1 reference genome, and the statisticalanalyses were performed using the previouslymentioned tools (edgeR, baySeq, and Cuffdiff 2). Finally,the identified genes were submitted to pathwayenrichment analysis. A total of 1,756, 1,161, and 3,389genes with differential gene expression were identifiedwhen using edgeR, baySeq, and Cuffdiff 2, respectively.A total of 122 genes were identified by the overlappingof the 3 methods; however, only the platelet activationpresented a significantly enriched pathway. Fromthe results, we suggest the FCER1G, GNAI2, ORAI1,and VASP genes shared among the 3 methods in thispathway for posterior biological validation.