Implementation of a liquid handler that can increase capacity of SARS-CoV-2 sequencing in animals with COVID-19.

实施液体处理程序，可以提高对感染 COVID-19 的动物进行 SARS-CoV-2 测序的能力。

• 批准号: 10827694
• 负责人: Brianna Stenger
• 金额: $ 6.02万
• 依托单位: NORTH DAKOTA STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-07-01 至 2024-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10827694
• 关键词: Implementation; liquid; handler; increase; capacity

SUMMARY The overall goal of this project is to purchase equipment that will increase capacity and speed up the library prep workflow and whole genome sequencing of the SARS-CoV-2 virus in companion animals by implementing an automated library prep process (NEBNext® ARTIC SARS-CoV-2 Companion Kit with ARTIC primers) and adding higher computing capabilities. Automating the library prep process with an affordable and versatile Opentron OT-2 liquid handling robot, in a one-way sequencing workflow, will benefit the laboratory by increasing throughput; improving sample consistency; minimizing contamination; freeing up hands-on time; reducing technician strain and fatigue; and minimize tech errors. Installation of a high-end computer workstation dedicated to sequencing and bioinformatics will significantly speed up the basecalling process and SARS-CoV-2 strain identification. This equipment proposal has three specific aims. 1) Purchase and install an Opentron OT-2 liquid handling robot in the new NDSU-VDL Sequencing Laboratory Section to maintain a one-way next-generation sequencing (NGS) workflow that will minimize contamination. The NDSU-VDL is familiar with the operation of OT-2 robots and hands-on library preparation. 2) Write a custom protocol in Python script for the OT-2 robot to automate the library prep steps for the NEBNext ARTIC SARS-CoV-2 Companion Kit for Oxford Nanopore Technologies (MinION) sequencers. The script will be made freely available to OT-2 users through protocol.io and/or github. 3) Purchase and install a high-end computer workstation to run MinION sequencers, complete basecalling, and for downstream bioinformatic analyses on SARS-CoV-2 companion animal samples (i.e. feline and canine respiratory swabs).

摘要 该项目的总体目标是购买设备，以提高产能和 加快SARS-CoV-2文库准备工作和全基因组测序 通过实施自动化的图书馆准备过程，在同伴动物中感染病毒 (带有ARTIC引物的NEBNext®ARTIC SARS-CoV-2伴侣试剂盒)和添加更高 计算能力。通过经济实惠且功能齐全的 Openton OT-2液体搬运机器人，在单向排序工作流程中，将使 实验室通过增加产量；提高样品的一致性；最大限度地减少污染； 解放动手时间；减少技术人员的紧张和疲劳；并最大限度地减少技术错误。 安装一个专门用于测序和生物信息学的高端计算机工作站将 大大加快了基本检测过程和SARS-CoV-2毒株鉴定。这 设备提案有三个具体目标。1)购买并安装Openton OT-2液体 搬运机器人在新的NDSU-VDL测序实验室段保持单向 下一代测序(NGS)工作流程将最大限度地减少污染。NDSU-VDL 熟悉OT-2机器人的操作和动手编写图书馆。2)编写定制 用于OT-2机器人的Python脚本中的协议，用于自动执行NEBNext的库准备步骤 用于牛津纳米孔技术(MINION)测序仪的Artic SARS-CoV-2伴侣试剂盒。 该脚本将通过Protocol.io和/或GitHub免费提供给OT-2用户。3) 购买并安装运行Minion测序仪的高端计算机工作站，完成 用于SARS-CoV-2伴生动物的下游生物信息学分析 样本(即猫和狗的呼吸道拭子)。