Transcription Factor Binding Sites 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 an 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 Cells were grown according to the approved ENCODE cell culture protocols (http://genome.ucsc.edu/ENCODE/protocols/cell/mouse). Enrichment and Library Preparation Chromatin immunoprecipitation was performed according to Ren Lab ChIP Protocol (http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf). Library construction was performed according to Ren Lab Library Protocol (http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf). Sequencing and Analysis Samples were sequenced on Illumina Genome Analyzer II, Genome Analyzer IIx and HiSeq 2000 platforms for 36 cycles. Image analysis, base calling and alignment to the mouse genome version mm9 were performed using Illumina's RTA and Genome Analyzer Pipeline software. Alignment to the mouse genome was performed using ELAND or Bowtie (Langmead et al., 2009) with a seed length of 25 and allowing up to two mismatches. Only the sequences that mapped to one location were used for further analysis. Of those sequences, clonal reads, defined as having the same start position on the same strand, were discarded. BED and wig files were created using custom perl scripts.

本数据集由DNA元件百科全书（Encyclopedia of DNA Elements, ENCODE）生成。若对本数据集存在疑问，请直接联系提交实验员Yin Shen，邮箱：[e-mail]。若对与本数据集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（Chromatin Immunoprecipitation sequencing, ChIP-seq，Robertson等，2007）技术，在多种C57Bl/6小鼠组织及原代细胞中鉴定转录因子结合位点与染色质修饰谱，实现了小鼠基因组顺式调控元件的全面解析，所涉样本包括骨髓、小脑、大脑皮层、心脏、肾脏、肝脏、肺脏、脾脏、小鼠胚胎成纤维细胞（MEFs）以及胚胎干细胞（ES细胞）。
具体而言，Ren课题组针对RNA聚合酶II（RNA polymerase II, PolII）、共激活蛋白p300、绝缘子蛋白CTCF以及两种染色质修饰标记H3K4me3与H3K4me1开展了检测。上述分子已被证实可用于识别启动子、增强子与绝缘子元件（Barski等，2007；Blow等，2010；Heintzman等，2009；Kim等，2007；Kim等，2005a；Visel等，2009）。其中，H3K4me3或PolII信号富集是活性启动子的强标志性特征；启动子区域外存在的p300或H3K4me1信号可作为增强子的标记；而CTCF结合位点则被视为潜在绝缘子元件的标志性特征。
针对每一种组织中的每一种转录因子或染色质修饰标记，本研究均开展了至少两次生物学重复实验。每项实验可产生2000万至3000万条单克隆唯一定位标签。
关于本数据集的使用条款与条件，请参阅以下链接：http://www.genome.gov/27528022 及 http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf。
细胞培养严格遵循经批准的ENCODE细胞培养方案（http://genome.ucsc.edu/ENCODE/protocols/cell/mouse）。
富集分析与文库制备：染色质免疫共沉淀实验按照Ren实验室的ChIP实验方案（http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf）执行；文库构建则依照Ren实验室的文库制备方案（http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf）完成。
测序与数据分析：样本采用Illumina Genome Analyzer II、Genome Analyzer IIx及HiSeq 2000测序平台进行36个循环的测序。图像分析、碱基识别以及比对至小鼠基因组mm9版本的步骤均通过Illumina的RTA与Genome Analyzer Pipeline软件完成。小鼠基因组比对使用ELAND或Bowtie（Langmead等，2009）工具执行，设置种子长度为25且允许最多2个错配。仅保留唯一定位的序列用于后续分析，其中，定义为在同一链上具有相同起始位置的克隆reads将被丢弃。本研究使用自定义Perl脚本生成BED与wig格式文件。