학술논문
Systems Biology Analyses in Chicken: Workflow for Transcriptome and ChIP-Seq Analyses Using the Chicken Skin Paradigm
Document Type
Chapter
Source
Avian and Reptilian Developmental Biology: Methods and Protocols. 08/15/2017. 1650:87-100
Subject
Language
English
ISSN
1064-3745
1940-6029
1940-6029
Abstract
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.