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Systems Biology Analyses in Chicken: Workflow for Transcriptome and ChIP-Seq Analyses Using the Chicken Skin Paradigm
Yung-Chih Lai1,2,3, Randall B Widelitz4, Cheng-Ming Chuong5,4,6
1Integrative Stem Cell Center, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan. yungchihlai@gmail.com.
Methods in Molecular Biology (Clifton, N.J.)
|August 16, 2017
Summary
This study presents a comprehensive workflow for analyzing messenger RNA sequencing (mRNA-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) data in chickens. The workflow provides essential guidelines for researchers studying gene expression and chromatin regulation in avian species.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- High-throughput sequencing technologies like mRNA sequencing (mRNA-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) are crucial for exploring biological phenomena at high resolution.
- While these next-generation sequencing (NGS) methods are widely applied in model organisms such as mice and humans, their application in other species, like chickens, is less documented.
Purpose of the Study:
- To establish a standardized workflow for RNA-Seq and ChIP-Seq data analysis specifically tailored for chicken studies.
- To provide detailed guidelines for processing and interpreting NGS data from chicken skin appendage tissue, serving as a model system.
Main Methods:
- Development of a bioinformatics pipeline for RNA-Seq analysis, including quality control, alignment, quantification, normalization, and differential gene expression analysis.
- Outline of a ChIP-Seq analysis pipeline covering quality control, alignment, peak calling, super-enhancer identification, and differential enrichment analysis.
Main Results:
- A complete workflow for both RNA-Seq and ChIP-Seq analyses in chickens has been assembled.
- Guidelines and pipelines are presented for key steps in NGS data processing and interpretation for avian research.
Conclusions:
- The developed workflow facilitates high-resolution molecular and genomic studies in chickens using established NGS technologies.
- This resource aims to enhance the application and understanding of RNA-Seq and ChIP-Seq in avian research, particularly in areas like skin appendage development.
