Skip to main content
eScholarship
Open Access Publications from the University of California

Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies.

  • Author(s): Ponzielli, Romina
  • Boutros, Paul C
  • Katz, Sigal
  • Stojanova, Angelina
  • Hanley, Adam P
  • Khosravi, Fereshteh
  • Bros, Christina
  • Jurisica, Igor
  • Penn, Linda Z
  • et al.
Abstract

High-throughput, microarray-based chromatin immunoprecipitation (ChIP-chip) technology allows in vivo elucidation of transcriptional networks. However this complex is not yet readily accessible, in part because its many parameters have not been systematically evaluated and optimized. We address this gap by systematically assessing experimental-design parameters including antibody purity, dye-bias, array-batch, inter-day hybridization bias, amplification method and choice of hybridization control. The combined performance of these optimized parameters shows a 90% validation rate in ChIP-chip analysis of Myc genomic binding in HL60 cells using two different microarray platforms. Increased sensitivity and decreased noise in ChIP-chip assays will enable wider use of this methodology to accurately and affordably elucidate transcriptional networks.

Many UC-authored scholarly publications are freely available on this site because of the UC's open access policies. Let us know how this access is important for you.

Main Content
Current View