PacBio RS Single Molecule, Real-Time (SMRT) DNA Sequencer

PacBio RS 单分子实时 (SMRT) DNA 测序仪

• 批准号: 8247675
• 负责人: SUZANNE SANDMEYER
• 金额: $ 60万
• 依托单位: UNIVERSITY OF CALIFORNIA-IRVINE
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-05-01 至 2013-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8247675
• 关键词: Administrator; Alternative Splicing; Animal Model; Area; Bioinformatics; California; Cancer Center; Chemicals; Commit; Cost Sharing; Custom; DNA; DNA Modification Process; DNA Resequencing; Detection; Development; Disease; Funding; Future; Gene Chips; Gene Expression; Genetic Recombination; Genetic Variation; Genome; Genomics; Grant; Haplotypes; Hereditary Disease; Housing; Human; Informatics; Location; Mediating; Methods; Modification; Monitor; Morphologic artifacts; Pattern; RNA; RNA Sequences; RNA Splicing; Reaction; Reading; Regenerative Medicine; Research Personnel; Sampling; Sequence Analysis; Single Nucleotide Polymorphism; System; Technology; Time; Training; Transcript; Transcriptional Regulation; Translations; United States National Institutes of Health; Virulence; base; instrument; meetings; new technology; operation; polymerization; programs; single molecule

DESCRIPTION (provided by applicant): We request funds toward the purchase of a PacBio RS Single Molecule, Real-Time, (SMRT) DNA sequencer. The specific advantages of the PacBio RS are: 1) no requirement for prior PCR amplification of sample DNA avoids associated problematic artifacts; 2) long-range polymerization enables sequencing of regions containing repeats, de novo assembly, and RNA seq of alternatively spliced transcripts; 3) direct detection of DNA modifications eliminates errors introduced by alternative chemical methods; and 4) potentially wide range of future single-molecule applications, including direct sequencing of RNA and direct monitoring of translation step times. The UCI Genomics High-Throughput Facility (GHTF) has been in existence for twelve years, providing custom medium format array, Affymetrix GeneChip array, and now Illumina format high- throughput sequencing to users within and outside of the UCI campus. Thus, it is an established base from which to introduce new sequencing technologies to the Southern California region. The PacBio RS is complementary rather than overlapping with the currently available Illumina technology in the GHTF, As a consequence of PacBio RS acquisition, twenty-five investigators would be directly enabled to perform projects in the areas of: 1) genome resequencing to identify bacterial virulence determinants that occur through DNA modification and recombination-mediated mechanisms; 2) model organism genome resequencing to study the relationship between recombination, repeated sequences and single-nucleotide polymorphism (SNP)-related genetic variation; 3) localized human haplotype determination to understand the relationship between cis-acting genetic variation and disease; 4) direct sequence analysis of modified DNA to understand the relationship between modification and gene expression; 4) long-range reads to determine alternative splicing patterns which underlie transcriptional regulation in development and disease; and 5) future applications to other single molecule reactions with fluorescent substrates, Funds have been committed by the campus to complete purchase of the PacBio instrument and extended warranty and to support a technician in the facility and a systems administrator for the bioinformatics pipeline. This is essentially an extension of the very successful, high throughput sequencing program initiated with the last NIH Shared Instrument Grant for the GAIIx sequencing platform. With that funding and cost sharing, the IGB informatics pipeline was established as was a Cancer Center Bioinformatics group and last year the Center for Regenerative Medicine cooperated with the GHTF to support a trade-up to the current Illumina HiSeq 2000, which is now in operation. In summary, the UCI Genomics and High-Throughput Facility is the ideal location in which to house this exciting new technology: trained staff, strong informatics, knowledgeable users and applications that are not met by current, more established technologies.

描述（由申请人提供）：我们请求资金购买 PacBio RS 单分子实时 (SMRT) DNA 测序仪。 PacBio RS 的具体优点是： 1) 不需要事先对样品 DNA 进行 PCR 扩增，避免了相关的有问题的伪影； 2) 长程聚合能够对包含重复的区域进行测序、从头组装以及选择性剪接转录本的 RNA seq； 3）直接检测DNA修饰，消除了替代化学方法引入的错误； 4) 未来潜在的广泛单分子应用，包括 RNA 的直接测序和翻译步骤时间的直接监测。 UCI 基因组学高通量设施 (GHTF) 已存在 12 年，为 UCI 校园内外的用户提供定制中型芯片、Affymetrix GeneChip 芯片以及现在的 Illumina 格式高通量测序。因此，它是向南加州地区引入新测序技术的既定基地。 PacBio RS 与 GHTF 目前可用的 Illumina 技术是互补而非重叠。收购 PacBio RS 后，25 名研究人员将能够直接执行以下领域的项目：1) 基因组重测序以识别细菌毒力通过 DNA 修饰和重组介导的机制发生的决定因素； 2）模型生物基因组重测序，研究重组、重复序列和单核苷酸多态性（SNP）相关遗传变异之间的关系； 3）局部人类单倍型测定，以了解顺式作用遗传变异与疾病之间的关系； 4）对修饰后的DNA进行直接序列分析，了解修饰与基因表达之间的关系； 4) 长程读取以确定发育和疾病中转录调控基础的选择性剪接模式； 5) 未来应用于其他荧光底物单分子反应，校园已承诺提供资金来完成 PacBio 仪器的购买和延长保修期，并为该设施的技术人员和生物信息学管道的系统管理员提供支持。这本质上是对 GAIIx 测序平台的最后一次 NIH 共享仪器资助启动的非常成功的高通量测序计划的延伸。凭借这些资金和成本分摊，IGB 信息学管道以及癌症中心生物信息学小组得以建立，去年再生医学中心与 GHTF 合作支持升级至目前正在运行的 Illumina HiSeq 2000 。总之，UCI 基因组学和高通量设施是容纳这项令人兴奋的新技术的理想场所：训练有素的员工、强大的信息学、知识渊博的用户和当前更成熟的技术无法满足的应用程序。

项目成果

Multi-tissue RNA-Seq Analysis and Long-read-based Genome Assembly Reveal Complex Sex-specific Gene Regulation and Molecular Evolution in the Manila Clam.

• DOI: 10.1093/gbe/evac171
• 发表时间: 2022-12-07
• 期刊: GENOME BIOLOGY AND EVOLUTION
• 影响因子: 3.3
• 作者: Xu, Ran;Martelossi, Jacopo;Smits, Morgan;Iannello, Mariangela;Peruzza, Luca;Babbucci, Massimiliano;Milan, Massimo;Dunham, Joseph P.;Breton, Sophie;Milani, Liliana;Nuzhdin, Sergey, V;Bargelloni, Luca;Passamonti, Marco;Ghiselli, Fabrizio
• 通讯作者: Ghiselli, Fabrizio