Genome-wide analysis of gene expression in the paraventricular nucleus of Sim1-Cre specific DNMT3a deletion mice

Analysis of gene expression in the paraventricular nucleus in the hypothalamus (PVH) of WT and Sim1-Cre specific DNMT3a deletion mice. Results provide important information about genes regulated by DNMT3a. For the gene expression profiling, total RNA was extracted from PVH of WT and Sim1-Cre specific DNMT3a deletion mice (C57BL6 background) at 6 weeks old using Qiagen RNeasy Lipid Tissue Mini Kit (Qiagen) and Phase Lock Gel (5 Prime Inc., Gaitherburg, MD). To make sure reproducibility and biological significance, triple hybridizations were performed for each genotype with the RNA from 3 indipendent PVH samples, each sample contains RNA from 5 animals. Genomics and Microarray Core Facility at UTSW (http://microarray.swmed.edu/) checked RNA quality with Bioanalyzer Chip and processed the samples for hybridization with Illumina Mouse-6 V2 BeadChip (Illumina Inc., San Diego, CA). We used GeneSpring GX (Agilent Technologies, Santa Clara, CA) for data analysis.本研究针对野生型（Wild Type, WT）与Sim1-Cre特异性DNMT3a敲除小鼠的下丘脑室旁核（paraventricular nucleus, PVH）开展基因表达分析，所得结果可为DNMT3a调控的相关基因提供关键研究信息。 在基因表达谱分析环节，研究人员以6周龄、C57BL/6背景的野生型与Sim1-Cre特异性DNMT3a敲除小鼠的PVH组织为材料，使用Qiagen RNeasy脂质组织迷你试剂盒（Qiagen）与Phase Lock Gel（5 Prime Inc.，马里兰州盖瑟斯堡）提取总RNA。为保障实验可重复性与生物学意义，针对每种基因型，均采用3份独立的PVH组织样本RNA进行三次杂交实验，每份样本包含5只小鼠的总RNA。 UTSW基因组学与微阵列核心实验室（http://microarray.swmed.edu/）采用Bioanalyzer芯片对RNA质量进行质检，并使用Illumina Mouse-6 V2微珠芯片（Illumina Inc.，加利福尼亚州圣迭戈）完成样本杂交处理。本研究采用GeneSpring GX（安捷伦科技有限公司，加利福尼亚州圣克拉拉）开展数据分析。