Identification of Transcription Factor ALY-2::GFP Binding Regions in L1. Caenorhabditis elegans

modENCODE_submission_3384 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP217(official name : OP217 genotype : unc119(ed3);wgIs217(aly-2:TY1 EGFP FLAG;unc119) outcross : 3 transgene : aly-2 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ALY-2::EGFP fusion protein is expressed in the correct aly-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ALY-2 transcription factor. made_by : Mihail Sarov ); Developmental Stage: fed L1; Genotype: unc119(ed3);wgIs217(aly-2:TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; Transgene: aly-2; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene aly-2; Strain OP217(official name : OP217 genotype : unc119(ed3);wgIs217(aly-2:TY1 EGFP FLAG;unc119) outcross : 3 transgene : aly-2 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ALY-2::EGFP fusion protein is expressed in the correct aly-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ALY-2 transcription factor. made_by : Mihail Sarov ); temp (temperature) 20 degree celsius

modENCODE_submission_3384
本次提交源自Michael Snyder主持的modENCODE项目。modENCODE项目完整列表可参见http://www.genome.gov/26524648。
项目目标：本项目旨在鉴定秀丽隐杆线虫（Caenorhabditis elegans，C. elegans）中300种转录因子的DNA结合位点。每个转录因子基因均携带有相同的GFP（绿色荧光蛋白，Green Fluorescent Protein）融合蛋白标签，可用于验证转基因动物中该基因的正确时空表达模式。随后使用抗GFP抗体对各菌株进行染色质免疫沉淀（Chromatin Immunoprecipitation, ChIP）实验，结合的DNA采用Solexa GA2技术进行深度测序。数据使用条款与规范请参阅http://www.genome.gov/27528022 及 http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf。

实验整体设计：
实验类型：ChIP-seq（染色质免疫沉淀测序）
生物来源：
菌株：OP217（官方名称：OP217；基因型：unc119(ed3);wgIs217(aly-2:TY1 EGFP FLAG;unc119)；回交次数：3；转基因元件：aly-2；标签：基因枪标签（Bombard tag）：GFP::3xFlag）
菌株构建说明：该菌株的转基因元件由德国蒂宾根马克斯·普朗克细胞生物学研究所的Mihail Sarov利用Tony Hyman的重组工程流水线构建所得。所得质粒用于对unc-119(ed3)菌株进行基因枪转化。ALY-2::EGFP融合蛋白可按照aly-2基因的正确时空表达模式进行表达。本菌株用于ChIP-seq实验，以定位ALY-2转录因子的体内结合位点。构建者：Mihail Sarov
发育阶段：喂食期L1幼虫；基因型：unc119(ed3);wgIs217(aly-2:TY1 EGFP FLAG;unc119)；性别：雌雄同体；转基因元件：aly-2
实验因素：发育阶段为喂食期L1幼虫；靶基因为aly-2；菌株OP217（官方名称：OP217；基因型：unc119(ed3);wgIs217(aly-2:TY1 EGFP FLAG;unc119)；回交次数：3；转基因元件：aly-2；标签：Bombard tag：GFP::3xFlag；菌株构建说明：该菌株的转基因元件由德国蒂宾根马克斯·普朗克细胞生物学研究所的Mihail Sarov利用Tony Hyman的重组工程流水线构建所得。所得质粒用于对unc-119(ed3)菌株进行基因枪转化。ALY-2::EGFP融合蛋白可按照aly-2基因的正确时空表达模式进行表达。本菌株用于ChIP-seq实验，以定位ALY-2转录因子的体内结合位点。构建者：Mihail Sarov）；培养温度：20摄氏度