Lai Yung-Chih, Widelitz Randall B, Chuong Cheng-Ming
Integrative Stem Cell Center, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan.
Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
Methods Mol Biol. 2017;1650:87-100. doi: 10.1007/978-1-4939-7216-6_5.
With advances in molecular biology, various biological phenomena can now be explored at higher resolution using mRNA sequencing (RNA-Seq) and chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq), two powerful high-throughput next-generation sequencing (NGS) technologies. While methods are used widely in mouse, human, etc., less information is available in other animals, such as the chicken. Here we assemble a workflow of the RNA-Seq and ChIP-Seq analyses for the chicken studies using chicken skin appendage tissue as an example. We present guidelines for RNA-Seq quality control, alignment, quantification, normalization, and differentially expressed gene analysis. In the meantime, we outline a bioinformatics pipeline for ChIP-Seq quality control, alignment, peak calling, super-enhancer identification, and differential enrichment analysis.
随着分子生物学的发展，现在可以使用mRNA测序（RNA-Seq）和染色质免疫沉淀结合高通量测序（ChIP-Seq）这两种强大的高通量下一代测序（NGS）技术，以更高的分辨率探索各种生物学现象。虽然这些方法在小鼠、人类等中广泛使用，但在其他动物如鸡中可用的信息较少。在这里，我们以鸡皮肤附属器组织为例，组装了用于鸡研究的RNA-Seq和ChIP-Seq分析工作流程。我们提出了RNA-Seq质量控制、比对、定量、标准化和差异表达基因分析的指南。同时，我们概述了用于ChIP-Seq质量控制、比对、峰识别、超级增强子鉴定和差异富集分析的生物信息学流程。
