title: The Overlooked Fact: Fundamental Need for Spike-In Control for Virtually All Genome-Wide Analyses.
abstract: Genome-wide analyses of changes in gene expression, transcription factor occupancy on DNA, histone modification patterns on chromatin, genomic copy number variation, and nucleosome positioning have become popular in many modern laboratories, yielding a wealth of information during health and disease states. However, most of these studies have overlooked an inherent normalization problem that must be corrected with spike-in controls. Here we describe the reason why spike-in controls are so important and explain how to appropriately design and use spike-in controls for normalization. We also suggest ways to retrospectively renormalize data sets that were wrongly interpreted due to omission of spike-in controls.
authors.affiliation: Institute for Academic Medicine, Houston, Texas, USA Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, The Methodist Hospital Research Institute, Houston, Texas, USA Weill Cornell Medicine, New York, New York, USA.
authors.forename: Kaifu
authors.initials: K
authors.lastname: Chen
authors.affiliation: Department of Epigenetics and Molecular Carcinogenesis, University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA Weill Cornell Medicine, New York, New York, USA.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Hu
authors.affiliation: Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Xia
authors.affiliation: Institute for Academic Medicine, Houston, Texas, USA Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, The Methodist Hospital Research Institute, Houston, Texas, USA Weill Cornell Medicine, New York, New York, USA.
authors.forename: Dongyu
authors.initials: D
authors.lastname: Zhao
authors.affiliation: Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.affiliation: Department of Epigenetics and Molecular Carcinogenesis, University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA Weill Cornell Medicine, New York, New York, USA jet2021@med.cornell.edu.
authors.forename: Jessica K
authors.initials: JK
authors.lastname: Tyler
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation / Q000379:methods; D056915:DNA Copy Number Variations; D055106:Genome-Wide Association Study / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods; D017423:Sequence Analysis, RNA / Q000379:methods