RNAseq comparison of the J and N (Taconic) substrains of C57BL/6 reveals substantial differences in endogenous Murine Leukemia Virus expression

C57BL/10J and C57BL/6NJ display an ~810 kb region of CNV spanning GRCm38 13:65.79–66.60 Mb, which extends to ~1.15 Mb in C57BR/cdJ (13:65.45–66.60 Mb). These deletions occur within a cluster of KRAB Zinc Finger Proteins (ZFPs) and cover the Gv1 locus, which controls expression of endogenous Murine Leukemia Viruses (MLVs). Here, we use RNAseq to compare the expression profiles of identically-housed C57BL/6J and C57BL/6NTac.