Next-generation sequencing facilitates quantitative analysis of CreAlbMYC and CreAlbScarb2F/FMYC mice liver tissue transcriptomes

ABSTRACT: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analyse the differential genes and pathways in liver tissue of CreAlbMYC and CreAlbScarb2F/FMYC mice by using RNA-seq. Methods: CreAlbMYC and CreAlbScarb2F/FMYC liver tissue mRNA profiles were generated by deep sequencing, using Illumina Novaseq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with following methods: Alignment by using HISAT2, IGV was used to view the mapping result by the Heatmap, histogram, scatter plot or other style, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including GO enrichment analysis and KEGG. Conclusions: Our study represents the first detailed analysis of CreAlbMYC and CreAlbScarb2F/FMYC liver tissue transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

ORGANISM(S): Mus musculus

PROVIDER: GSE207671 | GEO | 2023/08/11

REPOSITORIES: GEO