Chapter title |
Systems Biology Analyses in Chicken: Workflow for Transcriptome and ChIP-Seq Analyses Using the Chicken Skin Paradigm
|
---|---|
Chapter number | 5 |
Book title |
Avian and Reptilian Developmental Biology
|
Published in |
Methods in molecular biology, January 2017
|
DOI | 10.1007/978-1-4939-7216-6_5 |
Pubmed ID | |
Book ISBNs |
978-1-4939-7215-9, 978-1-4939-7216-6
|
Authors |
Yung-Chih Lai, Randall B. Widelitz, Cheng-Ming Chuong |
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. |
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