Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies.
Nucleic Acids Res
; 36(21): e144, 2008 Dec.
Article
in En
| MEDLINE
| ID: mdl-18940864
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.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Oligonucleotide Array Sequence Analysis
/
Chromatin Immunoprecipitation
Limits:
Humans
Language:
En
Journal:
Nucleic Acids Res
Year:
2008
Type:
Article
Affiliation country:
Canada