The Bioinformatics and Single Cell Analysis Core

总结 消化和肝病研究中心的生物信息学和单细胞核心（BSCAC）（CU- DLDRC）旨在提高我们对推动消化系统发展的机制的理解， 疾病基于单细胞的空间转录组学与创新的生物信息学分析相结合， 改变我们理解消化系统疾病中动态和多维生物过程的能力 并提供深入了解复杂的细胞-细胞，配体-受体和基因调控网络， 健康和疾病。BSCAC将提供最先进的人类和小鼠测序数据分析， 远远超出了大多数CU-DLDRC实验室的能力。为此，BSCAC将为其成员提供 以消化器官为重点的批量、单细胞（sc）、单核（sn）和单类器官RNA分析， 测序（RNA-seq），scATAC-seq和空间转录组学，以及细胞-细胞的创新分析 相互作用和转录主调节器。了解这些过程可能会提供新的 诊断和/或治疗干预的机会。通过链接BSCAC的多核工作流 临床生物库和研究中心（CBRC），类器官和细胞培养中心（OCCC）和生物成像 用于分析患者、细胞和类器官样本的核心（BIC），BSCAC将实现翻译和多功能 学科研究。BSCAC将通过以下方式使CU-DLDRC及其成员受益匪浅：（i）提供成本- 有效和优先获得最先进的分析;（二）使CU-DLDRC研究人员能够执行 消化道上皮生物学，稳态和相互作用的前沿研究，有密切联系， CU-DLDRC的中心主题;（iii）为转化研究和合作提供平台 （四）教育和培训CU-DLDRC成员，试点和 可行性获奖者，以及他们在这个快速发展的创新技术和新发展的实验室 领域BSCAC将由在生物信息学和单细胞分析方面具有良好记录的科学家领导。博士 彼得西姆斯，系统生物学副教授，将担任主任和博士罗伯特施瓦贝，教授 医学部副主任BSCAC将是一个利用率很高的资源，CU-DLDRC成员中有92% 表示在调查中使用。BASCAC将通过这些相互关联的具体措施， 目的：为CU-DLDRC成员提供批量RNA-seq的消化器官聚焦生物信息学分析， 来自人和小鼠样品的sc/snRNA-seq和空间转录组学数据（目的1）。提供CU-DLDRC 成员具有先进的消化器官为重点的生物信息学分析细胞间相互作用，转录 主调节器和细胞轨迹（目标2）。为CU-DLDRC成员提供培训和教育， 讲习班和研讨会（目标3）。通过这些目标以及与其他CU-DLDRC的无缝集成 BSCAC将为CU-DLDRC的使命做出贡献，并为其成员提供重大利益。

SUMMARY The Bioinformatics and Single Cell Core (BSCAC) in the Digestive and Liver Disease Research Center (CU- DLDRC) seeks to enhance our understanding of the mechanisms that drive the development of digestive diseases. Single cell-based and spatial transcriptomics in conjunction with innovative bioinformatic analyses are transforming our ability to understand dynamic and multidimensional biological processes in digestive diseases and provide deep insights into the complex cell-cell, ligand-receptor and gene regulatory networks that regulate health and disease. BSCAC will provide state-of-the-art analyses of human and murine sequencing data that go far beyond the capability of most individual CU-DLDRC labs. For this, the BSCAC will provide its members with digestive organ-focused analyses of bulk, single-cell (sc), single-nucleus (sn) and single-organoid RNA- sequencing (RNA-seq), scATAC-seq, and spatial transcriptomics, as well as innovative analyses of cell-cell interactions and transcriptional master regulators. Understanding these processes may provide novel opportunities for diagnosis and/or therapeutic interventions. Through multi-core workflows that link the BSCAC to the Clinical Biobanking & Research Core (CBRC), the Organoid& Cell Culture Core (OCCC) and Bioimaging Core (BIC) for analyses of patient, cell and organoid samples, the BSCAC will enable translational and multi- disciplinary research. BSCAC will significantly benefit the CU-DLDRC and its members by (i) providing cost- effective and prioritized access to state-of-the-art analyses; (ii) empowering CU-DLDRC researchers to perform cutting-edge research on digestive tract epithelial biology, homeostasis and interactions, there closely linking to the central theme of the CU-DLDRC; (iii) contributing a platform for translational research and collaboration between clinical and basic researchers; and (iv) educating and training CU-DLDRC members, Pilot and Feasibility awardees, and their labs in innovative technologies and novel developments in this rapidly evolving field. The BSCAC will be led by scientists with strong track records in bioinformatics and single cell analysis. Dr. Peter Sims, Associate Professor of Systems Biology, will serve as director and Dr. Robert Schwabe, Professor of Medicine, as associate director. BSCAC will be a highly utilized resource with 92% of CU-DLDRC members indicating use in surveys. BASCAC will contribute to the CU-DLDRC’s mission through these interrelated Specific Aims: To provide CU-DLDRC members with digestive organ-focused bioinformatic analyses of bulk RNA-seq, sc/snRNA-seq and spatial transcriptomics data from human and mouse samples (Aim 1). To provide CU-DLDRC members with advanced digestive organ-focused bioinformatic analyses of cell-cell interactions, transcriptional master regulator and cell trajectories (Aim 2). To provide training and education to CU-DLDRC members via workshops and seminars (Aim 3). Through these Aims as well as seamless integration with the other CU-DLDRC cores, BSCAC will contribute to the mission of the CU-DLDRC and provide significant benefit to its members.