SpBase: A Database System For Echinoderm Genome Information

SpBase：棘皮动物基因组信息数据库系统

• 批准号: 8267958
• 负责人: Robert Andrew Cameron
• 金额: $ 58.3万
• 依托单位: CALIFORNIA INSTITUTE OF TECHNOLOGY
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-06-15 至 2017-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8267958
• 关键词: Ally; Area; Biological; Conflict (Psychology); Data; Data Set; Databases; Development; Elements; Genbank; Gene Cluster; Gene Expression Profile; Gene Expression Regulation; Gene Order; Gene Structure; Genes; Genome; Genomics; Goals; Health; Homeostasis; Human Genome; Individual; Information Systems; Internet; Laboratories; Link; Lytechinus variegatus; Measurement; Medicine; Organism; Peptides; Process; Protein Isoforms; Publishing; Regulator Genes; Research; Scientist; Sea Urchins; Strongylocentrotus purpuratus; Structure; System; Tissue-Specific Splicing; Translating; Update; biomineralization; college; comparative; comparative genomics; gene discovery; genome sequencing; genome-wide; indexing; interest; nano-string; network models; research study; web-accessible

DESCRIPTION (provided by applicant): The overall aim of this project is to gather, collate and present genomic information for echinoderm species including the reference, Strongylocentrotus purpuratus (Sp) through an easily managed web information system (http://spbase.org). These efforts are directly focused to provide the bench scientist with up to date information on the genome sequence, gene structures, expression data and functional information in order to facilitate experiments to study gene regulation in development. Originally a draft sequence for the reference was undertaken by the Baylor College of Medicine, Human Genome Sequencing Center (BCM-HGSC) and published in 2006 (Sea Urchin Genome Sequencing Consortium, 2006). Today efforts in this area are both challenging and interesting in view of the large body of emerging sequence information on the reference and allied species. An entirely new assembly of the Sp genome has been submitted to Genbank and awaits further annotation at SpBase. However, preliminary measurements indicate that this version is so much more complete that it can reveal scientifically interesting elements of genome organization that were unattainable previously. Individual laboratory transcriptome sequencing projects for many species are appearing at a great rate. These datasets are seldom analyzed past the experimental question for which they were originally conducted, yet they can provide genome wide information on gene structure such as tissue specific splicing isoforms. In support of the BCM-HGSC, we have provided material for additional genome sequencing projects including Allocentrotus fragllis, S. franciscanus, Lytechinus variegatus, Eucidaris tribuloides and Patiria miniata. New sequence data for all of these species has been procured and in some cases already posted to Genbank. This is the material that will enrich the offering of SpBase provided it is carefully managed and posted.

描述（由申请人提供）：本项目的总体目标是通过一个易于管理的网络信息系统（http：//www.example.com）收集、整理和展示棘皮动物物种的基因组信息，包括参比品，紫球海胆（Sp）。spbase.org这些努力直接集中于为实验室科学家提供关于基因组序列、基因结构、表达数据和功能信息的最新信息，以促进研究发育中基因调控的实验。最初，参考序列草案由贝勒医学院人类基因组测序中心（BCM-HGSC）承担，并于2006年发表（海胆基因组测序联盟，2006）。今天，这方面的努力既 鉴于参考物种和近缘物种的大量新出现的序列信息，这具有挑战性和有趣性。一个全新的组装的Sp基因组已提交给Genbank，并等待进一步的注释在SpBase。然而，初步的测量表明，这个版本是如此的完整，它可以揭示科学上有趣的基因组组织的元素，这是以前无法实现的。许多物种的单个实验室转录组测序项目正在以很高的速度出现。这些数据集很少被分析过去的实验问题，他们最初进行，但他们可以提供基因结构的基因组范围内的信息，如组织特异性剪接异构体。为了支持BCM-HGSC，我们为其他基因组测序项目提供了材料，包括Allocentrotus fragllis，S。franciscanus、Lytechinus variegatus、Eucidaris tribioides和Patiria miniata。所有这些物种的新序列数据已经获得，在某些情况下已经发布到Genbank。这是将丰富SpBase提供的材料，只要它被仔细管理和发布。