Bioinformatics Core

生物信息学核心摘要/摘要 波特兰酒精研究中心(PARC)研究项目将产生大量基因 来自多个物种和处理条件的表达和表观遗传学数据。生物信息学的核心 (C002)将在管理和分析这些数据方面发挥不可或缺的作用，从而能够识别 酒精暴露和酗酒风险的基因组标志物。C002的主要功能是提供 支持每个项目内的主端点的基础分析，通过以下方式提供更高级别的推断 跨PARC项目集成数据，并通过将PARC数据与 公开可用的数据资源。 C002将与PARC调查人员合作，设计、排除故障并执行最佳计算实践 分析适用于每个项目的主要终点的管道。堆芯的实验设计和 分析服务包括：1)生物信息学，如DNA-和RNA-SEQ读取比对、差异 表达和途径分析、甲基化和表观遗传分析、数据集成和定制脚本 写作；以及2)生物统计学，如生物标记物、纵向、存活率和高通量/高维 组学分析。在特定研究期间，这两个类别下的服务通常是集成的。每一项分析都是 定制以最适合项目和调查人员的需求。 此外，C002将通过定制整合大数据资源来增强单个PARC项目 在公共领域中可用。C002将下载并组织可用的单细胞RNA测序 (scRNA-seq)相关小鼠大脑区域的数据，创建了一份细胞类型特定表达的图谱，可以 用于精细定位P001和P002中观察到的驱动差异表达模式的细胞类型。 同样，C002将存储来自人类和小鼠的公开可用表观遗传信息，这将使 P001、P002、P003和P004中的表达和甲基化 更大的基因组注释集(例如CHIP-SEQ、ATAC-SEQ等)。最后，C002将执行跨项目 通过搜索可能在物种之间共享的信号进行整合，首先通过评估共同基因 在小鼠和猕猴实验中确定的设置或路径，并作为最后的转换步骤，评估 基于PARC的见解与大量关于酒精的人类遗传学数据的融合 使用无序。

Bioinformatics Core Summary/Abstract The Portland Alcohol Research Center (PARC) research projects will generate large amounts of gene expression and epigenetic data from multiple species and treatment conditions. The Bioinformatics Core (C002) will play an integral role in the management and analysis of these data, enabling the identification of genomic markers of alcohol exposure and risk for alcohol abuse. The key functions of C002 will be to provide foundational analyses to enable the primary endpoints within each project, provide higher-order inference by integrating data across PARC projects, and to augment these analyses by integration of PARC data with publicly available data resources. C002 will work with PARC investigators to design, troubleshoot, and execute best-practices computational analysis pipelines appropriate for the primary endpoints for each project.The core's experimental design and analysis services include: 1) Bioinformatics such as DNA- and RNA-seq read alignment, differential expression and pathway analysis, methylation and epigenetic analyses, data integration, and custom script writing; and 2) Biostatistics such as biomarker, longitudinal, survival, and high-throughput/high-dimensional omics analysis. Services under these two categories are often integrated during a given study. Each analysis is customized to best fit the needs of the project and investigator. Furthermore, C002 will augment individual PARC projects by bespoke integration of big data resources available in the public domain. C002 will download and organize available single-cell RNA-sequencing (scRNA-seq) data from relevant mouse brain regions, creating an atlas of cell type-specific expression that can be used for fine-mapping the cell types driving differential expression patterns observed in P001 and P002. Likewise, C002 will host publicly available epigenetic information from human and mouse, which will allow expression and methylation in P001, P002, P003 and P004 to be annotated and contextualized with a much larger set of genomic annotations (e.g. ChIP-seq, ATAC-seq, etc). Finally, C002 will perform cross-project integration by searching for signals that may be shared across species, first by assessing for common gene sets or pathways identified in mouse and macaque experiments, and, as a final translational step, assessing the convergence of PARC-based insights with the vast amount of human genetics data emerging on Alcohol Use Disorder.