NGS analysis of gene regulation in animal models

Commonly used inbred mouse strains, also known as the classical inbred strains such as C57BL/6J (B6) derived predominantly from Western European wild mice, Mus musculus domesticus. On the other hand, an inbred strain MSM/Ms (MSM) was established at NIG from Japanese wild mouse, M. m. molossinus. Recently, we have found a vast quantity of genomic differences such as SNPs and short indels between B6 and MSM. Presumably, as a consequence of its genomic differences, MSM has detected unique phenotypes of many quantitative traits compared to those of B6. The aim of this project is to analyze mouse inter-subspecific variation of gene expression regulation that participates in various quantitative traits. At the beginning, we have conducted genome-wide transcriptome analysis for the study of body growth associated phenotypes using growing bone samples containing cartilage cells in the knee joints from B6 and MSM, and their hybrid cross.