Dataset Information

New Insights from Transcriptome Profiling of Bovine Vaginal Epithelial Cell Response to Isolated Lactobacillus

ABSTRACT: Purpose: The goals of this study is to investigate host cell responses treated with lactobacillus in various molecular pathways by RNA-Seq and real-time quantitative PCR (RT-qPCR) methods to and evaluate protocols for optimal high-throughput data analysis. Methods: mRNA profiles of bovine vaginal epithelial cells treated with lactobacillus and control cells were generated by sequencing, in triplicate, utilizing Illumina HiSeq 4000 platform. The raw RNA-seq data was filtered to remove adaptor contamination, low quality bases, and undetermined bases utilizing Cutadapt software.The filtered reads were aligned and mapped to the reference genome using Hisat 2.0. RT-qPCR validation was performed using TaqMan and SYBR Green assays. Results: The transcription profiling results showed that 296 differentially expressed genes (DEGs) were significantly altered, of which 170 were upregulated and 126 downregulated. Gene ontology (GO) enrichment analysis of the DEGs revealed a significant enrichment of 424 GO terms throughout the differentiation process (p< 0.05). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs were mainly involved in signal transduction, immune endocrine systems, transport and catabolism, as well as metabolism and genetic information processing. We found a relatively high number of genes enriched in protein processing in the endoplasmic reticulum and IL-17 signaling pathway, as well as antigen processing and presentation. DEGs that enriched into pathways were verified by RT-qPCR. The highest number of DEGs participated in protein processing in pathways involving the endoplasmic reticulum of which might be a major factor causing the adhesion of lactobacillus to cells and pathogenic inhibition. Conclusions:Our study provides new insights on the interaction between lactobacillus and host cells, emphasizing the importance of novel candidate pathways involving the protein processing in endoplasmic reticulum and analyzing the possible anti-pathogenic mechanisms of the SQ0048 strain that inhibit pathogenic colonization.

ORGANISM(S): Bos taurus

PROVIDER: GSE127808 | GEO | 2019/03/10

REPOSITORIES: GEO

ACCESS DATA

Similar Datasets

Project description:purpose:The goals of this study is to investigate rat quadriceps muscle responses treated with different catgut embedding acupoint in various molecular pahtways by RNA-seq and real-time quantitative PCR methods and evaluaate protocols for optimal high-throughput data analysis. Methods:mRNA profiles of rat quadriceps muscle responses treated with catgut embedding acupoint 1 and 2 group,treadmill group and control were generated by sequencing, in sextuplicate, utilizing Illumina HiSeq 4000 platform. The raw RNA-seq data was filtered to remove adaptor contamination, low quality bases, and undetermined beses utilizing Cutadapt software. The filtered reads were aligned and mapped to the reference genome using Hisat 2.0. RT-qPCR validation was performed using SYBR green assays. Results:The transcription profiling results showed that there were 346 differentially expressed genes (DEGs) between the A and B groups. These included 221 up-regulated DEGs and 125 down-regulated DEGs. There were 363 DEGs between the B group and the C, which included 144 up-regulated DEGs and 219 down-regulated DEGs. There were 458 DEGs between the B group and D which included 248 up-regulated DEGs and 210 down-regulated DEGs. Through GO functional annotation, the DEGs were divided into three categories: cellular components, biological processes, and molecular functions. The above three functions were further divided into positive regulation of transcription by RNA polymerase II, and RNA polymerase II on transcription. Negative regulation, participation in nuclear synthesis, synthesis with cytoplasm, participation in extracellular exosome synthesis, participation in protein binding, and participation in metal ion binding, etc. After enrichment analysis, 16 metabolic pathways were found to be significantly enriched (p<0.05), which included chemical carcinogenesis, metabolism of cytochrome P450 to exogenous substances, circadian entrainment, circadian rhythm, protein digestion and absorption, PPAR Signaling pathways, drug metabolism - cytochrome P450, parathyroid hormone synthesis, secretion and action, steroid hormone biosynthesis, leishmaniasis, arachidonic acid metabolism, bile secretion, measles, linoleic acid metabolism, fat digestion and absorption, and fluid shear stress and atherosclerosis. By inspecting the bubble enrichment plot, we decided that the following would be important targets of our future studies: protein digestion and absorption; PPAR signaling pathway; synthesis, secretion and action of parathyroid hormone and other metabolic pathways.DEGs that enriche into pathways were verified by RT-qPCR. Conclusions: Our study provides new insights on the interaction between catgut embedding acupoint and rat quadriceps muscle responses.

Dataset Information

New Insights from Transcriptome Profiling of Bovine Vaginal Epithelial Cell Response to Isolated Lactobacillus

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure