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.
CITATION STYLE
Lai, Y. C., Widelitz, R. B., & Chuong, C. M. (2017). Systems biology analyses in chicken: Workflow for transcriptome and ChIP-Seq analyses using the chicken skin paradigm. In Methods in Molecular Biology (Vol. 1650, pp. 87–100). Humana Press Inc. https://doi.org/10.1007/978-1-4939-7216-6_5
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