RNAseq analysis of two independent strains of C57BL/6J-Plat-/- mice and wild-type C57BL/6J.

The ability to generate defined null mutations in mice revolutionized the analysis of gene function in mammals. However, gene-deficient mice generated by using 129-derived embryonic stem (ES) cells may carry large segments of 129 DNA, even when extensively backcrossed to reference strains, such as C57BL/6J, and this may confound interpretation of experiments performed in these mice. Tissue plasminogen activator (tPA), encoded by the PLAT gene, is a fibrinolytic serine protease that is widely expressed in the brain. A large number of neurological abnormalities have been reported in tPA-deficient mice. The studies here compare genes differentially expressed in the brains of Plat-/- mice from two independent Plat-/- mouse derivations to wild-type C57BL/6J mice. One strain denoted "Old" was constructed in ES cells from a 129 mouse and backcrossed extensively to C57BL/6J, and one denoted "New" Plat-/- mouse was constructed using zinc finger nucleases directly in the C57BL/6J-Plat-/- mouse strain. We identify a significant set of genes that are differentially expressed in the brains of Old Plat-/- mice that preferentially cluster in the vicinity of Plat on chromosome 8, apparently linked to more than 20 Mbp of DNA flanking Plat being of 129 origin. No such clustering is seen in the New Plat-/- mice. Whole-transcriptome profiling of the cerebral cortex of wild-type control C57BL/6J mice and two independent Plat-/- mice strains on the C57BL/6J background.在小鼠体内构建定向无效突变（null mutations）的技术，彻底革新了哺乳动物基因功能的研究范式。然而，利用129品系胚胎干细胞（embryonic stem cells, ES cells）制备的基因敲除小鼠，即便经多轮回交至C57BL/6J等参考品系，仍可能携带大片段129品系DNA序列，这会干扰此类小鼠实验结果的解读。 组织型纤溶酶原激活剂（tissue plasminogen activator, tPA）是由PLAT基因编码的纤维蛋白溶解丝氨酸蛋白酶，在大脑中广泛表达。已有大量研究报道tPA敲除小鼠存在多种神经功能异常。 本研究对比了两种独立构建的PLAT敲除（Plat-/-）小鼠大脑中的差异表达基因，并以野生型C57BL/6J小鼠作为对照。其中一款被命名为“Old”的品系，通过129小鼠的ES细胞构建，并经多轮回交至C57BL/6J品系获得；另一款被命名为“New”的PLAT敲除小鼠，则是利用锌指核酸酶（zinc finger nucleases）直接在C57BL/6J背景小鼠体内构建得到。 我们发现，Old品系PLAT敲除小鼠的大脑中存在一批显著差异表达的基因，这些基因优先聚集于8号染色体上PLAT基因的邻近区域，显然与PLAT基因侧翼超过20兆碱基对（Mbp）的129品系来源DNA序列相关。而New品系PLAT敲除小鼠中未观察到此类基因聚集现象。 本数据集包含野生型对照C57BL/6J小鼠，以及两种独立的C57BL/6J背景PLAT敲除小鼠品系的大脑皮层全转录组谱分析数据。