The overlooked fact: Fundamental need for spike-in control for virtually all genome-wide analyses

Kaifu Chen, Zheng Hu, Zheng Xi, Dongyu Zhao, Wei Li, Jessica K. Tyler

Research output: Contribution to journalArticle

62 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)662-667
Number of pages6
JournalMolecular and Cellular Biology
Volume36
Issue number5
DOIs
StatePublished - 2016

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

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