Transcriptome Profiling and Targeted Genic Improvement of the X. tropicalis Genom

热带 X. 基因组的转录组分析和有针对性的基因改良

• 批准号: 8460905
• 负责人: Ken W.Y. Cho
• 金额: $ 48.52万
• 依托单位: YALE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-08-01 至 2015-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8460905
• 关键词: Adult; Animal Model; Bioinformatics; ChIP-seq; Chromosome Mapping; Collaborations; Communities; DNA-Protein Interaction; Data; Databases; Development Plans; Developmental Cell Biology; Developmental Gene; Diploidy; Effectiveness; Embryo; Embryonic Development; Exons; Fostering; Future; Gene Expression; Gene Expression Profile; Gene Structure; Genes; Genetic; Genetic Markers; Genome; Genomics; Health; Human; Human Biology; International; Maps; Messenger RNA; Methods; Modeling; Molecular Profiling; Mutation; Mutation Detection; Paper; Phenotype; Process; Rana; Regulator Genes; Regulatory Element; Relative (related person); Research; Research Personnel; Resolution; Resources; Sorting - Cell Movement; Staging; System; Technology; Time; Tissues; Transcript; United States National Institutes of Health; Work; Xenopus; Xenopus laevis; base; biological systems; cost; expression cloning; gene discovery; genetic analysis; genome annotation; genome sequencing; genome-wide; human disease; improved; meetings; mutant; skills; tool; transcriptome sequencing

DESCRIPTION (provided by applicant): Xenopus is a premier system for studying early vertebrate developmental and cell biology. The availability of genomic sequence has enabled genomic and genetic analyses. However, annotation of gene models in the X. tropicalis genome remains poor, hampering these efforts. In this proposal, we will perform targeted sequencing to annotate the genic part of the genome. This will include 1) transcript sequencing to assemble the transcriptome and identify temporal gene expression, 2) sequence capture to fill gaps in the genic portions of the genome, and 3) SNP identification to facilitate genetics. Improved annotation of the genic portion of the X. tropicalis genome assembly will enable many priorities of the Xenopus community that are outlined in the 2009 Xenopus White Paper: 1) it will make a more complete ORFeome possible 2) greatly facilitate genetics and 3) improve the assembly of the X. laevis genome. For these reasons, the 2009 Xenopus Community White Paper lists "Improvement of the X. tropicalis genome sequence and annotation" as an essential resource.

描述(申请人提供)：非洲爪哇是研究早期脊椎动物发育和细胞生物学的首选系统。基因组序列的可获得性使基因组和遗传分析成为可能。然而，对热带疟原虫基因组中的基因模型的注释仍然很差，阻碍了这些努力。在这个提案中，我们将执行定向测序来注释基因组的基因部分。这将包括1)转录测序以组装转录组并识别时间基因表达，2)序列捕获以填补基因组基因部分的空白，以及3)SNP识别以促进遗传学。改进的热带爪哇按蚊基因组组装基因部分的注释将使2009年非洲爪哇白皮书中概述的非洲爪哇群落的许多优先事项成为可能：1)它将使更完整的ORO成为可能；2)极大地促进遗传学和3)改进非洲爪哇按蚊基因组的组装。出于这些原因，2009年非洲爪哇社区白皮书将“热带爪哇爪哇鼠基因组序列和注释的改进”列为一项重要资源。