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）：该项目的总体目的是通过易于管理的Web信息系统（http://spbase.org）收集，整理和呈现棘皮动物物种的基因组信息。这些努力直接集中于为基因组序列，基因结构，表达数据和功能信息提供最新信息，以促进实验以研究开发中的基因调节。最初是由贝勒医学院，人类基因组测序中心（BCM-HGSC）进行的，并于2006年出版（海胆基因组测序联盟，2006年）。今天在这方面的努力都是 鉴于有关参考物种和相关物种的大量新兴序列信息，具有挑战性和有趣。 SP基因组的全新组装已提交给GenBank，并在SPBASE上进行了进一步的注释。但是，初步测量表明，此版本更加完整，以至于它可以揭示以前无法实现的基因组组织的科学有趣元素。许多物种的单个实验室转录组测序项目的出现速度很高。这些数据集很少经过最初进行的实验问题，但它们可以提供有关基因结构（例如组织特异性剪接同工型）的基因组广泛信息。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Fragllis，S。Franciscanus，Lytechinus Variegatus，Eucidaris Tribuloides和Patiria Miniata。所有这些物种的新序列数据已被购买，在某些情况下已经发布到GenBank。如果仔细管理和张贴，这将是丰富SPBASE产品的材料。