@inbook{120f5a651c4142d8831342aa46d35d6b,
title = "RNA-seq and expression arrays: Selection guidelines for genome-wide expression profiling",
abstract = "The development of genome-wide gene expression profiling technologies over the past two decades has produced great opportunity for researchers to explore the transcriptome and to better understand biological systems and their perturbation. In this chapter we provide an overview of microarray and massively parallel sequencing technologies and their application to gene expression analysis. We discuss factors that impact expression data generation and analysis that which should be considered in the application of these technology platforms. We further present the results of a simple illustration study to highlight performance similarities and differences in expression profiling of protein-coding mRNAs with each platform. Based on technical and analytical differences between the two platforms, reports in the literature comparing arrays and RNA-Seq for gene expression, and our own example study and experience, we provide recommendations for platform selection for gene expression studies.",
keywords = "Differential expression, Expression array, Expression profiling, Massively parallel sequencing, Microarray, RNA-seq",
author = "Jessica Minnier and Pennock, {Nathan D.} and Quichen Guo and Pepper Schedin and Harrington, {Christina A.}",
note = "Funding Information: The authors thank Julja Burchard for enthusiastic and thoughtful discussions on the design and content of the chapter. We thank Dr. Robert Searles for manuscript review and expert advice on RNA-Seq methods. We thank Caitlin Harrington-Smith for creative assistance with figures and Amy Carlos and Kristina Vartanian for excellent technical assistance. This work was supported in part by the OHSU Knight Cancer Institute (NIHNCI Cancer Center Support Grant P30 CA069533-17) and NIH/NCI R01CA169175 (to P. Schedin). Publisher Copyright: {\textcopyright} Springer Science+Business Media, LLC, part of Springer Nature 2018.",
year = "2018",
doi = "10.1007/978-1-4939-7834-2_2",
language = "English (US)",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "7--33",
booktitle = "Methods in Molecular Biology",
}