Next Generation Sequencing Facilitates Analysis of The Mouse Oocyte?Cumulus cells and Blastocyst Transcriptomes From PM2.5 Exposure Group And Filtrated Air Group

Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare mouse NGS-derived oocyte?cumulus cell and blastocyst transcriptome profiling (RNA-seq) between PM2.5 exposure group and Filtrated air group Methods: mouse oocyte?cumulus cell and blastocyst mRNA profiles were generated by deep sequencing, in triplicate for each stage, using Illumina Hi-Seq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9). Genes with adjusted P < 0.05 and fold-change (FC) = 2 were considered differentially expressed genes (DEGs). The oocyte transcriptome analysis showed that 467 DEGs (260 and 207 up- and down-regulated genes, respectively) were identified in the CAP group compared with the FA group. In the cumulus cell analysis, 592 DEGs (358 and 234 up- and down-regulated genes, respectively) were identified in the CAP group compared with the FA group. The blastocyst transcriptome analysis identified 448 DEGs (254 and 194 up- and down-regulated, respectively) in the CAP group compared with the FA group. Conclusions: Our study represents the first detailed analysis of mouse oocyte?cumulus cell and blastocyst transcriptomes, with biologic replicates, generated by RNA-seq technology between PM2.5 exposure group and Filtrated air group. Overall design: Mouse oocyte?cumulus cell and blastocyst mRNA profiles of PM2.5 exposure group and Filtrated air group were generated by deep sequencing, in triplicate, using Illumina Hi-Seq 2500