RNA-seq of Sall2 wild-type, heterozygous and knockout MEFs

Genetically engineered mice (GEM) are essential tools for understanding gene function and disease modeling. Due to historical reasons, gene targeting was at first done in embryonic stem cells (ESC) derived from the 129 family of inbred strains, leading to mixed background or congenic mice when crossed with C57BL/6 mice. Depending on the number of backcrosses and breeding strategies genomic segments from 129-derived ESC can be introgressed into the C57BL/6 genome at different levels, establishing a unique genetic makeup that needs characterization in order to obtain valid conclusions of experiments using GEM models. We sequenced wild-type (WT), heterozygous (Het) and knockout (KO) mouse embryonic fibroblasts (MEFs) from a knockout model of Sall2 (Sato A. et al, Zinc finger protein sall2 is not essential for embryonic and kidney development. Mol Cell Biol 2003, 23:62-69) maintained in a mixed background between C57BL/6J and 129P2OlaHsd mice. We also treated these cells with doxorubicin, as a global perturbation of the gene expression. With this schema, we aimed to detect genetic introgression of 129 mice onto C57BL/6J, KO-ligated variants (the so-called congenic footprint) and potential modifier genes. Sall2 wild-type (WT), heterozygous (Het) and knockout (KO) MEFs treated or not with doxorubicin 1 µM for 16 hours