MRLxSM eQTL in Liver by RMA on Ensembl transcripts

A QTL analysis between inbred mouse strains MRL/MpJ and SM/J was performed to identify genetic loci influencing high-density lipoprotein (HDL) cholesterol and triglycerides (TG) at eight weeks of age in F2 mice fed a chow diet. In order to narrow down lists of candidate genes, expression levels from liver tissue were used to test for differential expression among parental and F1 strains and to scan for eQTL in F2 animals. We provide evidence for Mppe1 (Chr 18) as an HDL QTL candidate gene and Cyp2d26 (Chr 15) as a TG QTL candidate gene. MRL/MpJ (MRL) mice were crossed with male SM/J (SM) mice; their progeny were intercrossed to produce 371 F2 animals. Of these, 282 F2 males and females were profiled with Affy Mouse Gene 1.0 ST arrays for an eQTL study. Three animals from each parental and the F1 strains from each sex, i.e. 18 in total, were also profiled for testing differential expression. A total of 300 samples are included in the dataset. The mice were weaned at 3 weeks on a chow diet. At 13 weeks of age, mice were single housed for 3 days and fasted for 4 hours prior to being sacrificed. Tissue collection was performed between noon and 1pm to avoid variations due to circadian rhythm.本研究针对近交系小鼠品系MRL/MpJ与SM/J开展数量性状位点(QTL)分析，旨在筛选饲喂标准饲料的F2代8周龄小鼠中，调控高密度脂蛋白(HDL)胆固醇与甘油三酯(TG)水平的遗传位点。为缩小候选基因集范围，本研究利用肝脏组织的基因表达水平，检测亲本与F1代品系间的差异表达情况，并对F2代个体开展表达数量性状位点(eQTL)扫描。本研究证实，Mppe1（18号染色体）可作为HDL相关QTL的候选基因，Cyp2d26（15号染色体）可作为TG相关QTL的候选基因。将MRL/MpJ（简称MRL）小鼠与雄性SM/J（简称SM）小鼠杂交，随后对其子代进行互交，共获得371只F2代个体。其中282只雌雄F2代个体通过Affy Mouse Gene 1.0 ST阵列开展表达谱分析，用于本项eQTL研究。每个亲本品系与F1代品系的各性别组均选取3只个体，总计18只，同样开展表达谱分析以检测差异表达情况。本数据集共包含300个样本。所有小鼠于3周龄时断奶，并饲喂标准饲料。小鼠于13周龄时单笼饲养3天，并处死前禁食4小时。组织样本采集于正午至下午1点之间进行，以避免昼夜节律带来的实验误差。