LSU Bioinformatics Workshop course materials

RNA sequencing (RNA-Seq) is a powerful tool that captures information about how organisms respond to stimuli in their environment at the molecular level. A common RNA-Seq approach involves isolating and sequencing all of the messenger RNA (mRNA) in a tissue sample taken from an organism. Researchers can compare patterns observed in RNA-Seq data to understand how individuals respond to the environment over minutes, hours, or days and how populations evolve in response to the environment over millions of years. The materials in this repository will guide users through an analysis of RNA-Seq data collected from two California populations of a copepod crustacean, Tigriopus californicus, that were exposed to different levels of salinity. Users will examine the contents of a fastq file that contains raw RNA-Seq data, determine the quality of the RNA-Seq data using a web-server, and test for significant differences in gene expression between the copepod populations using the R packages DESeq2, edgeR, and VennDiagram. The course materials were developed for the 2022 LSU Bioinformatics Workshop held at Louisiana State University, Baton Rouge, LA on July 17-22, hosted by Melissa DeBiasse and Morgan Kelly.

RNA测序（RNA sequencing, RNA-Seq）是一种强大的分子生物学研究工具，可精准捕捉生物体对环境刺激的响应信息。常见的RNA-Seq实验流程需要分离并测序从生物体组织样本中提取的全部信使RNA（messenger RNA, mRNA）。研究人员可通过比对不同样本的RNA-Seq观测数据模式，解析个体在数分钟、数小时乃至数天内的环境响应机制，以及种群在数百万年间的环境适应性演化规律。本存储库提供的教程材料将引导用户完成两组加利福尼亚种群桡足类甲壳动物——加州虎斑猛水蚤（Tigriopus californicus）——的RNA-Seq数据分析，该实验对象曾暴露于不同盐度水平的环境中。用户将依次完成以下操作：查看包含原始RNA-Seq数据的fastq文件内容，通过网页服务器评估该测序数据的质量，并使用R包DESeq2、edgeR与VennDiagram，检验这两个桡足类种群间的基因表达差异显著性。本课程材料专为2022年路易斯安那州立大学（Louisiana State University, LSU）生物信息学研讨会开发，该研讨会于2022年7月17日至22日在路易斯安那州巴吞鲁日的路易斯安那州立大学校园内举办，由Melissa DeBiasse与Morgan Kelly主持。