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Series GSE10114 Query DataSets for GSE10114
Status Public on Feb 01, 2008
Title Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
Project ENCODE
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by genome tiling array
Summary 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.

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This SuperSeries is composed of the SubSeries listed below.
Overall design Refer to individual Series
Web link
Citation(s) 18258921
BioProject PRJNA63447
Submission date Jan 09, 2008
Last update date Dec 28, 2012
Contact name Jason D Lieb
Phone (919) 843-3228
Fax (919) 962-1625
Organization name University of North Carolina at Chapel Hill
Department Department of Biology
Street address CB# 3280, 202 Fordham Hall
City Chapel Hill
State/province NC
ZIP/Postal code 27599-3280
Country USA
Platforms (6)
GPL2131 Nimblegen ENCODE Array
GPL3980 UC Davis Human ENCODE array
GPL4559 ENCODE NimbleGen hg17 tiling array
Samples (47)
GSM245281 No Ab Spike in DNA sample undiluted ENCODE NimbleGen hg17 tiling array (90899)
GSM245282 No Ab Spike in DNA sample diluted ENCODE NimbleGen hg17 tiling array (90899)
GSM245283 No Ab Spike in DNA sample diluted ENCODE NimbleGen hg17 tiling array (90951)
This SuperSeries is composed of the following SubSeries:
GSE9732 Spike-in Experiment for ChIP-chip Simulation
GSE9842 Systematic evaluation of variability in simulated ChIP-chip experiments
GSE9848 Systematic evaluation of variability in simulated ChIP-chip experiments Kevin_Encode

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE10114_GEOAccession.txt 2.6 Kb (ftp)(http) TXT
GSE10114_RAW.tar 1.4 Gb (http)(custom) TAR (of CEL, GFF, PAIR, TXT)
Raw data provided as supplementary file
Processed data included within Sample table

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