Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation [dataset 2]

In this study, we generated six whole-genome bisufite sequencing (WGBS) data that were colloced from Rumen Epithelial Primary Cells (REPC) before and after (24h) butytate treatment. By combining other types of data sets, inclduing six histone modifications, RNA polymerase II, CTCF-binding sites, DNA accessibility, and RNA-seq, we established the first global map of regulatory elements (15 chromatin states) and defined their coordinated activities in cattle. We, for the first time, were able to establish the correlation among nutritional elements, chromatin states, gene activities, and phenotypic outcomes. Overall design: Rumen primary epithelial cells were isolated from a two-week-old Holstein bull calf fed with milk replacer only. For butyrate treatment, 5 mM butyrate was added to the culture medium for 24-h. Briefly, DNA from REPC culture was isolated by phenol/chloroform extraction. DNA (100 ng) was bisulfite-converted and subjected to library preparation using the Pico Methyl-Seq™ Library Prep Kit (Zymo) following the instructions of the supplier. High-Sensitivity DNA chips were used to assess libraries for quality on the Agilent Bioanalyzer and quantified with Qubit fluorometer. Libraries were sequenced on an Illumina HiSeq2500 (150-bp paired-end sequencing).

在本项研究中，我们通过对瘤胃上皮原代细胞（REPC）在丁酸处理前（24小时）及处理后（24小时）进行了六组全基因组亚硫酸氢盐测序（WGBS）数据的生成，结合包括六种组蛋白修饰、RNA聚合酶II、CTCF结合位点、DNA可及性和RNA-seq在内的其他类型数据集，我们构建了首个牛的调控元件（15种染色质状态）的全景图，并定义了它们在协调活动中的功能。我们首次建立了营养元素、染色质状态、基因活性以及表型结果之间的关联。总体设计如下：从仅以代乳粉喂养的2周龄荷斯坦公犊的瘤胃上皮原代细胞中分离细胞。对于丁酸处理，将5 mM的丁酸添加至培养基中，持续24小时。简要来说，通过苯酚/氯仿提取法从REPC培养中分离DNA，并对100 ng的DNA进行亚硫酸氢盐转化，随后按照供应商的说明使用Pico Methyl-Seq™文库制备试剂盒（Zymo）进行文库制备。使用高灵敏度DNA芯片在Agilent Bioanalyzer上评估文库质量，并通过Qubit荧光计进行定量。文库在Illumina HiSeq2500上进行了150-bp配对末端测序。