RNA-Seq Analysis for Mouse Geneticists

Next-generation sequence analyses of transgenic mouse models present specific challenges to quantifying gene expression of exogenous coding regions, such as fluorescent reporters (GFP, tdTomato), or effector proteins (Cre, neo), because standard reference genomes lack the corresponding sequence information. DNASTAR Lasergene software has tools for efficient sequence editing of the targeted loci, generating matching genome templates for precise alignments of next-generation sequencing data. In this example, we studied RNA expression profiles in mouse cortical microglia of two different embryonic origins. One population was labeled with GFP only, the other population was labeled with GFP and tdTomato. Dissociated cells were isolated by FACS sorting and deep sequencing of the isolated RNA was performed on the Illumina platform. The presentation will demonstrate how SeqMan NGen and QSeq applications facilitate advanced bioinformatics analyses for mouse geneticists.