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Next Generation Sequencing For Quantitative Analysis Of Hepatic Transcriptomes In Response To Erythrodiol

ABSTRACT: Purpose: The goal of this study was to determine erythrodiol effect on hepatic transcriptome by comparing high-throughput data for tested group vs. control group. Method: Hepatic mRNA profile of two Apoe deficient male mice groups fed over 12 weeks with either western diet or same diet enriched with 10 mg/kg erythrodiol was analysed by Transcriptome sequencing using BGISEQ-500 platform. Sequence reads that passed quality filters were mapped onto reference genome, followed by novel gene prediction, SNP & INDEL calling and gene-splicing detection. Results: When using optimized Bioinformatics Workflow, mapping ratio for both tested groups was about 74%. There was no significant difference in SNPs between both groups. Splicing patterns _including Skipped Exon (SE), Alternative 5' Splicing Site (A5SS), Alternative 3' Splicing Site (A3SS), Mutually exclusive exons (MXE) and Retained Intron (RI) _allowed the production of a variety of DSGs with a total of 14,920 novel transcripts, 13,439 coding and 1,481 non coding transcripts. Coding genes showed 11,605 previously unknown splicing events for known genes and 1,834 coding transcripts previously unknown. DEGs were 554 in control group vs. 488 in erythrodiol group. Applying a 2-fold change and P value <0.001 led to 68 up regulated genes and 124 down-regulated genes. Gene Ontology Analysis of DEG With the GO annotation and functional enrichment classified DEGs to 3 main classification with liver-dependent properties. Altered expression of 21 genes was confirmed with RT-qPCR, demonstrating the high degree of sensitivity and accuracy of RNA-seq technique Conclusions: This study represents the first analysis of hepatic transcriptome in respond to erythrodiol. Result data confirm that RNA-Sequencing is a sensitive and accurate tool that provides a framework for comparative investigations of known and novel DEGs.

ORGANISM(S): Mus musculus

PROVIDER: GSE155163 | GEO | 2020/10/28

REPOSITORIES: GEO

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Next Generation Sequencing For Quantitative Analysis Of Hepatic Transcriptomes In Response To Erythrodiol

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