Dataset Information

Mining the Methylome for New Insights into Bovine Tuberculosis.

ABSTRACT: Mining the Methylome for New Insights into Bovine Tuberculosis.

PROVIDER: PRJEB67806 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	ERR12148526_1.fastq.gz	Fastqsanger.gz
	ERR12148526_2.fastq.gz	Fastqsanger.gz
	ERR12148527_1.fastq.gz	Fastqsanger.gz
	ERR12148527_2.fastq.gz	Fastqsanger.gz

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Project description: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.

Dataset Information

Mining the Methylome for New Insights into Bovine Tuberculosis.

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