Histone Modifications by ChIP-seq from ENCODE/LICR

This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Yin Shen mailto:[e-mail]). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:[e-mail]).This track shows a comprehensive survey of cis-regulatory elements in the mouse genome by using ChIP-seq (Robertson et al., 2007) to identify transcription factor binding sites and chromatin modification profiles in many mouse (C57Bl/6) tissues and primary cells, including bone marrow, cerebellum, cortex, heart, kidney, liver, lung, spleen, mouse embryonic fibroblast cells (MEFs) and embryonic stem (ES) cells.In specific, the Ren lab examined RNA polymerase II (PolII), co-activator protein p300, the insulator protein CTCF, and two chromatin modification marks H3K4me3 and H3K4me1 due to their demonstrated utilities in identifying promoters, enhancers and insulator elements (Barski et al., 2007; Blow et al., 2010; Heintzman et al., 2009; Kim et al., 2007; Kim et al., 2005a; Visel et al., 2009). Enrichment of H3K4me3 or PolII signals is a strong indicator of active promoter, while the presence of p300 or H3K4me1 outside of promoter regions has been used as a mark for enhancers. CTCF binding sites are considered as a mark for potential insulator elements. For each transcription factor or chromatin mark in each tissue, ChIP-seq was carried out with at least two biological replicates. Each experiment produced 20-30 million monoclonal, uniquely mapped tags.For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

本数据集由ENCODE项目生成。若对数据集本身存在疑问，请直接联系提交人Yin Shen（邮箱：[e-mail]）；若对本数据关联的基因组浏览器轨道存在疑问，请联系ENCODE项目组（邮箱：[e-mail]）。
本轨道通过染色质免疫共沉淀测序（ChIP-seq），结合Robertson等人2007年的研究方法，对小鼠基因组的顺式调控元件（cis-regulatory elements）开展全面图谱分析，以此鉴定转录因子结合位点（transcription factor binding sites）与染色质修饰谱（chromatin modification profiles）。本次研究检测的样本涵盖多株C57Bl/6品系小鼠的组织与原代细胞（primary cells），包括骨髓、小脑、皮层、心脏、肾脏、肝脏、肺、脾脏，以及小鼠胚胎成纤维细胞（mouse embryonic fibroblast，MEFs）与胚胎干细胞（embryonic stem，ES细胞）。
具体而言，Ren实验室针对RNA聚合酶II（RNA polymerase II，PolII）、共激活蛋白（co-activator protein）p300、绝缘子蛋白（insulator protein）CTCF，以及两种经典染色质修饰标记（chromatin modification marks）H3K4me3和H3K4me1展开了检测——上述因子与标记已被证实可用于鉴定启动子（promoter）、增强子（enhancer）及绝缘子元件（insulator elements）（Barski et al., 2007; Blow et al., 2010; Heintzman et al., 2009; Kim et al., 2007; Kim et al., 2005a; Visel et al., 2009）。其中，H3K4me3或PolII信号富集是活跃启动子的强力判定标志；启动子区域外出现的p300或H3K4me1信号，可作为增强子的特征标记；CTCF结合位点则被视为潜在绝缘子元件的标记。针对每一种转录因子或染色质标记，本研究在各组织中均开展了至少两次生物学重复实验（biological replicates），单次实验可产出2000万至3000万条单克隆唯一比对标签（monoclonal, uniquely mapped tags）。
关于本数据集的使用条款与条件，请参阅http://www.genome.gov/27528022 及 http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

搜集汇总

背景与挑战

背景概述

该数据集是由ENCODE项目生成的小鼠组蛋白修饰ChIP-seq数据，旨在全面调查小鼠基因组中的顺式调控元件，包括转录因子结合位点和染色质修饰谱。它覆盖了多种组织和细胞类型，如骨髓、心脏、肝脏和脾脏等，并重点关注H3K4me3、H3K4me1等标记以识别启动子和增强子，每个实验均包含至少两个生物学重复。