Bioinformatics Core

生物信息学核心摘要/摘要 波特兰酒精研究中心（PARC）的研究项目将产生大量的基因， 来自多个物种和处理条件的表达和表观遗传数据。生物信息学核心 （C 002）将在这些数据的管理和分析中发挥不可或缺的作用， 酒精暴露和酒精滥用风险的基因组标记。C 002的主要功能是提供 基础分析，使每个项目内的主要终点，提供高阶推理， 整合PARC项目的数据，并通过整合PARC数据来增强这些分析， 公开可用的数据资源。 C 002将与PARC研究人员合作设计、排除故障并执行最佳计算实践 分析管道适合每个项目的主要终点。核心的实验设计和 分析服务包括：1）生物信息学，如DNA和RNA-seq读段比对，差异分析， 表达和途径分析、甲基化和表观遗传分析、数据集成和自定义脚本 生物统计学，如生物标志物、纵向、存活和高通量/高维 组学分析这两类服务在特定研究中往往是综合的。每个分析都是 根据项目和调查人员的需要进行定制。 此外，C 002还将通过定制大数据资源的整合来增强PARC的各个项目 在公共领域可用。C 002将下载并组织可用的单细胞RNA测序 （scRNA-seq）数据，创建细胞类型特异性表达图谱， 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，C 002将承载来自人类和小鼠的公开可用的表观遗传信息，这将允许 P001、P002、P003和P004中的表达和甲基化进行注释，并与许多 更大的基因组注释集（例如ChIP-seq、ATAC-seq等）。最后，C 002将执行跨项目 通过搜索可能在物种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鉴定的组或途径，并且作为最后的翻译步骤， 基于PARC的见解与酒精领域出现的大量人类遗传学数据的融合 使用Disorder。

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.