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Series GSE127808 Query DataSets for GSE127808
Status Public on Mar 10, 2019
Title New Insights from Transcriptome Profiling of Bovine Vaginal Epithelial Cell Response to Isolated Lactobacillus
Organism Bos taurus
Experiment type Expression profiling by high throughput sequencing
Summary 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.
 
Overall design mRNA profiles of bovine vaginal epithelial cells treated with lactobacillus and control cells were generated by sequencing, in triplicate, utilizing Illumina HiSeq 4000 platform.
 
Contributor(s) Niu C
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Mar 04, 2019
Last update date Mar 10, 2019
Contact name chunyu Niu
E-mail(s) 1251674572@qq.com
Organization name Inner Mongolia Agricultural University
Street address college of inner mongolia agricultural university ,306 street zhao wu da ,huhhot ,inner mongolia,china
City Hohhot
ZIP/Postal code 010010
Country China
 
Platforms (1)
GPL23295 Illumina HiSeq 4000 (Bos taurus)
Samples (6)
GSM3639234 con1
GSM3639235 con2
GSM3639236 con3
Relations
BioProject PRJNA525435
SRA SRP187463

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE127808_genes_fpkm_expression.txt.gz 2.9 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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