TPD-seq:一种高吞吐量RNA-seq方法,用于从细胞系中导出转录基因起点的转录基因点
Krittika Mittal1, Ke Xu1, Samuel J Rulli2
1Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Canada.
概括
这项研究介绍了TPD-seq,这是一个工作流程,将细胞暴露与tPOD的RNA测序联系起来. 它成功地推导出了人类和鱼类细胞中常见化学物质的tPOD值,有助于毒性研究.
科学领域:
- 毒理学 毒理学 毒理学
- 基因组学就是基因组学.
- 计算生物学 计算生物学
背景情况:
- 越来越多的人对高通量体外实验的转录基因起点 (tPOD) 感兴趣.
- 需要民主化的tPOD研究方法.
- 现有的方法需要先进的生物信息学专业知识.
研究的目的:
- 概述和验证TPD-seq工作流程来导出tPOD值.
- 将基于微板的细胞暴露与RNA-seq和生物信息学分析联系起来.
- 为了证明TPD-seq与常见的毒性测试化学品的实用性.
主要方法:
- TPD-seq工作流:微板细胞培养 (Caco-2,Hep G2,RTgill-W1),商业RNA-seq套件,基于云的生物信息学 (ExpressAnalyst.ca).
- 适用于溶剂 (DMSO,甲醇) 和正控 (DCA,H2O2) 的应用.
- 对基因表达数据,曲线匹配和基因基准剂量计算的分析.
主要成果:
- 成功地映射RNA-seq可以读取蛋白质编码基因.
- 显著的差异表达基因百分比产生了基因基因基准剂量.
- 对于DMSO (31-155毫米),DCA (~5-76毫米) 和H2O2 (0.7-1.1毫米在Caco-2中,5-30毫米在Hep G2中) 的tPOD值.
- 暴露于DMSO产生了最强大的转录基因反应.
结论:
- TPD-seq为tPOD衍生提供了一个可扩展和可访问的工作流.
- 该方法适用于具有基本分子和细胞培养设施的实验室.
- 进一步的案例研究可以确定TPD-seq.的完整性能和可扩展性.
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