Epigenomics and DNA Sequencing

表观基因组学和 DNA 测序

• 批准号: 10253945
• 负责人: TREVOR K ARCHER
• 金额: $ 234.67万
• 依托单位: NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10253945
• 关键词: ATAC-seq; Architecture; Cell Nucleus; Cell Separation; ChIP-seq; Chromium; Chromosomes; Communities; Consultations; Cost Savings; Custom; DNA; DNA Sequence; DNA Sequencing Facility; DNA sequencing; Data; Data Analyses; Detection; Disease; Experimental Designs; Family; Gene Cluster; Gene Family; Genes; Genetic; Genome; Genomics; Germ Lines; Individual; Instruction; Investigation; Libraries; Link; Malignant Neoplasms; Malignant neoplasm of prostate; Methods; Mutagenesis; National Institute of Environmental Health Sciences; Outcome; Predisposition; Preparation; Process; Research; Research Personnel; Sampling; Scientist; Services; System; Time; Training; Variant; design; design and construction; epigenomics; genetic linkage; instrumentation; next generation sequencing; prostate carcinogenesis; single cell analysis; single cell sequencing; single-cell RNA sequencing; sperm protein; targeted sequencing; theories; transcriptome sequencing

The Epigenomics and DNA Sequencing Core Lab provides a variety of services to the NIEHS scientific community. For next-generation sequencing, the core produces hundreds of millions of short sequence reads of individual DNA molecules using the Illumina NovaSeq 6000, NextSeq 500 or Illumina's MiSeq platforms. The Core also performs high-throughput single cell sequencing on the 10X Genomics Chromium or for smaller scale single cell analysis using the Illumina/BioRad ddSeq instrumentation. The Core staff provides, instruction on NGS theory, consultation in experimental design, training of staff in various methods, expert advice in cost saving practices as well as expert advice on data interpretation and analysis of data. NIEHS scientists may request NextGen Sequencing by submitting project applications online. The applications will be reviewed by the core staff and/or the governance committee. The core will accept and process samples from the approved projects for sequencing. For DNA Sequencing, we aim to provide DNA sequence data to individual investigators in a timely manner. We also assist labs in SNP discovery, mutagenesis detection, custom primer design, expression construct design, and optimization of PCR. In addition to the services we provide, the Core has also collaborated with investigators at NCI to further understand the SPANX gene family. Genetic linkage studies indicate that germ line variations in a gene or genes on chromosome Xq27-28 are implicated in prostate carcinogenesis. The linkage peak of prostate cancer overlies a region of approximately 750 kb containing five SPANX genes (SPANX-A1, -A2, -B, -C, and -D) encoding sperm proteins associated with the nucleus; their expression was also detected in a variety of cancers. We continue to further characterize this region of the genome. We speculate that the predisposition to prostate cancer in X-linked families is an example of a genomic disease caused by a specific architecture of the SPANX gene cluster.

表观基因组学和DNA测序核心实验室为NIEHS科学界提供各种服务。对于下一代测序，核心使用Illumina NovaSeq 6000、NextSeq 500或Illumina的MiSeq平台产生单个DNA分子的数亿个短序列读数。 Core还可在10 X Genomics Chromium上进行高通量单细胞测序，或使用Illumina/BioRad ddSeq仪器进行较小规模的单细胞分析。核心工作人员提供NGS理论指导，实验设计咨询，各种方法的工作人员培训，成本节约实践的专家建议以及数据解释和数据分析的专家建议。NIEHS科学家可以通过在线提交项目申请来请求NextGen测序。申请将由核心工作人员和/或治理委员会审查。核心将接受和处理来自已批准项目的样本，以进行测序。 对于DNA测序，我们的目标是及时向个别研究人员提供DNA序列数据。我们还协助实验室进行SNP发现、诱变检测、定制引物设计、表达构建体设计和PCR优化。除了我们提供的服务，核心还与NCI的研究人员合作，以进一步了解SPAN基因家族。遗传连锁研究表明，染色体Xq 27 -28上的一个或多个基因的种系变异与前列腺癌发生有关。前列腺癌的连锁峰覆盖约750 kb的区域，该区域包含5个编码与细胞核相关的精子蛋白的SPAN X基因（SPAN X-A1、-A2、-B、-C和-D）;在多种癌症中也检测到它们的表达。我们将继续进一步描述基因组的这一区域。我们推测X连锁家族中前列腺癌的易感性是由SPAN基因簇的特定结构引起的基因组疾病的一个例子。