TY  - JOUR
A1  - Johnson, David S.
A1  - Li, Wei
A1  - Gordon, D. Benjamin
A1  - Bhattacharjee, Arindam
A1  - Curry, Bo
A1  - Ghosh, Jayati
A1  - Brizuela, Leonardo
A1  - Carroll, Jason S.
A1  - Brown, Myles
A1  - Flicek, Paul
A1  - Koch, Christoph M.
A1  - Dunham, Ian
A1  - Bieda, Mark
A1  - Xu, Xiaoqin
A1  - Farnham, Peggy J.
A1  - Kapranov, Philipp
A1  - Nix, David A.
A1  - Gingeras, Thomas R.
A1  - Zhang, Xinmin
A1  - Holster, Heather
A1  - Jiang, Nan
A1  - Green, Roland D.
A1  - Song, Jun S.
A1  - McCuine, Scott A.
A1  - Anton, Elizabeth
A1  - Nguyen, Loan
A1  - Trinklein, Nathan D.
A1  - Ye, Zhen
A1  - Ching, Keith
A1  - Hawkins, David
A1  - Ren, Bing
A1  - Scacheri, Peter C.
A1  - Rozowsky, Joel
A1  - Karpikov, Alexander
A1  - Euskirchen, Ghia
A1  - Weissman, Sherman
A1  - Gerstein, Mark
A1  - Snyder, Michael
A1  - Yang, Annie
A1  - Moqtaderi, Zarmik
A1  - Hirsch, Heather
A1  - Shulha, Hennady P.
A1  - Fu, Yutao
A1  - Weng, Zhiping
A1  - Struhl, Kevin
A1  - Myers, Richard M.
A1  - Lieb, Jason D.
A1  - Liu, X. Shirley
T1  - Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
Y1  - 2008/03/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 393 
EP  - 403 
DO  - 10.1101/gr.7080508 
VL  - 18 
IS  - 3 
UR  - http://genome.cshlp.org/content/18/3/393.abstract 
N2  - The most widely used method for detecting genome-wide protein–DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first objective analysis of tiling array platforms, amplification procedures, and signal detection algorithms in a simulated ChIP-chip experiment. Mixtures of human genomic DNA and “spike-ins” comprised of nearly 100 human sequences at various concentrations were hybridized to four tiling array platforms by eight independent groups. Blind to the number of spike-ins, their locations, and the range of concentrations, each group made predictions of the spike-in locations. We found that microarray platform choice is not the primary determinant of overall performance. In fact, variation in performance between labs, protocols, and algorithms within the same array platform was greater than the variation in performance between array platforms. However, each array platform had unique performance characteristics that varied with tiling resolution and the number of replicates, which have implications for cost versus detection power. Long oligonucleotide arrays were slightly more sensitive at detecting very low enrichment. On all platforms, simple sequence repeats and genome redundancy tended to result in false positives. LM-PCR and WGA, the most popular sample amplification techniques, reproduced relative enrichment levels with high fidelity. Performance among signal detection algorithms was heavily dependent on array platform. The spike-in DNA samples and the data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated. 
ER  -