Genomic Sciences Shared Resource

基础研究小组 CORE 006-基因组科学共享资源 项目摘要/摘要 基因组科学共享资源(GSSR)提供所需的高级基因组学技术 支持范德比尔特-英格拉姆癌症中心(VICC)成员开展的全方位癌症研究。 该设施利用大量的基因分型和测序为研究人员提供最先进的服务 技术平台。该设施的一个独特功能是可获得和定制许多主要 基因组学技术平台，在分析方法上提供了非凡的灵活性。GSSR服务 产品线包括基因分型、高通量基因分型、桑格测序和“下一代”测序， 包括全基因组、全外显子组、靶向重测序、RNA-SEQ、CHIP-SEQ和miR-SEQ。GSSR 还与调查人员合作，帮助开发新的测序策略，如PRO-SEQ (精密全球核连续测序)和CHIP-Exo(染色质免疫沉淀+核酸外切酶 足迹-测序)。随着这些技术和标准的发展，GSSR不断更新 有能力保持在这些领域的领先地位。该资源拥有一批最先进的资源 仪器，包括两个HiSeq 2500测序仪，两个MiSeq测序仪和到高级 计算集群。通常，其中一个HiSeq仪器被分配到常规运行模式以完成 要求如大型exome项目，而第二个仪器则用在快速运行模式下，非常方便 较小项目的快速周转，最常见的是RNA-Seq分析。GSSR提供了高水平的 为各级用户提供培训和咨询，包括提供“工作室”以审查与癌症有关的项目 来自寻求在这一资源中使用技术的调查人员。因此，每个项目都会收到定制的审查和 来自经验丰富的员工的意见。在这一领域，数据存储和数据访问至关重要，而 GSSR已完全集成到该机构的数据中心和超级计算集群中，以实现快速和 高效的数据传输和分析。数据生成只是成功实验的第一步， 调查人员在数据分析领域的复杂程度各不相同。GSSR基本上提供了 原始数据(遵循QC流程以确保质量)提供给复杂的用户群体，但也提供数据集 对许多小组进行大量的标准分析。用户可以访问工作站，这是一个大面板 还提供了商业分析工具的情况和这些工具的使用方向。最重要的是， GSSR与量化科学共享资源(QSSR)共享一名生物信息学家和数据管理员； 工作人员被安置在GSSR，为调查人员提供个性化的数据分析指导，并 当需要定制分析时，与QSSR提供的高级分析服务对接。

BASIC RESEARCH GROUP CORE 006 – GENOMIC SCIENCES SHARED RESOURCES PROJECT SUMMARY/ABSTRACT The Genomic Sciences Shared Resource (GSSR) provides advanced genomics technologies required to support the full range of cancer research conducted by Vanderbilt-Ingram Cancer Center (VICC) members. This facility provides investigators with state-of-the-art services utilizing a myriad of genotyping and sequencing technology platforms. A unique feature of the facility is the availability and customizability of numerous major genomics technology platforms, which offer exceptional flexibility in analytical approaches. The GSSR service lines include genotyping, high-throughput genotyping, Sanger sequencing and “next-generation” sequencing, including whole genome, whole exome, targeted re-sequencing, RNA-seq, ChIP-seq and miR-seq. The GSSR also works with investigators to aid in the development of new sequencing strategies such as PRO-seq (precision global nuclear run-on-sequencing) and ChIP-Exo (chromatin immunoprecipitation + exonuclease footprinting-sequencing). As these technologies and standards evolve, the GSSR continues to update capabilities to stay at the forefront of these fields. The resource maintains a bevy of state-of-the-art instruments, including two HiSeq 2500 sequencers, two MiSeq sequencers and links to the advanced computing cluster. Typically, one of the HiSeq instruments is assigned to conventional run mode to accomplish requests such as large exome projects, while the second instrument is used in rapid run mode to facilitate very rapid turnover of smaller projects, most commonly RNA-Seq analysis. The GSSR provides a high level of training and consultation for users of all levels, including providing “studios” to review cancer-related projects from investigators seeking to use technologies in this resource. Thus, each project receives custom review and input from a highly experienced staff. Storage of data and access to data is paramount in this area, and the GSSR has fully integrated into the institution’s data center and supercomputing cluster to enable rapid and efficient transfer and analysis of data. Data generation is only the first step to a successful experiment and investigators have varying levels of sophistication in the area of data analysis. The GSSR provides essentially raw data (following QC processes to ensure quality) to sophisticated user groups, but also provides data sets with a significant amount of standard analysis to many groups. Access for users to workstations, a large panel of commercial analytical tools and orientation to the uses of these tools is also provided. Most importantly, the GSSR shares a bioinformatician and data manager with the Quantitative Sciences Shared Resource (QSSR); staff are housed in the GSSR to provide investigators with personalized guidance for data analysis and to interface with the advanced analytical services provided by the QSSR when customized analysis is needed.