GSE183383
Quantitative Analysis of Cerebral Cortex Transcriptomes of BrapcKO Mice and their Wildtype-like Control Mice by Next-Generation Sequencing
Purpose: Transcriptome profiling (RNA-seq) was performed in this study in order to assess differential gene expressions resulting from Brap loss of function in murine cerebral cortex. Methods: Cerebral cortical mRNA profiles of 3-month-old Emx1-Cre-mediated Brap conditional knockout mice (BrapcKO) and their Cre-negative control littermates (Brap flox Cre-) were generated by next-generation sequencing, using Illumina HiSeq4000. Five BrapcKO and five control samples were analyzed. The quality of raw sequencing data was assessed using FastQC. Sequence reads that passed quality filters were analyzed by several methods, including DESeq2, edgeR, and Iimma, to discover differentially expressed genes. Results: We obtained more than 30 million sequence reads per sample that are uniquely mapped to the mouse reference genome (build mm10). After alignment of reads, expression levels of individual genes were quantified and estimated using subread::featureCounts. With the removal of lowly expressed genes using the threshold at least 10 raw read counts, 14,276 out of 21,969 annotated, valid mouse genes were retained for further analysis. Data were analyzed using several state-of-the-art tools, including DESeq2, edgeR, and Iimma, with a fold change =1.5 and FDR < 0.1. We collected overlapped differentially expressed mRNA genes detected with more than one method, and identified 811 differentially expressed genes between BrapcKO and control group. Conclusions: Our study represents detailed analysis of transcriptomes, with biologic replicates, generated by RNA-seq technology. The data provide insight into the neurological defects of BrapcKO mice. Overall design: Cerebral cortical mRNA profiles of 3-month BrapcKO mice and their wildtype-like control littermates.