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Series GSE9848 Query DataSets for GSE9848
Status Public on Dec 13, 2007
Title Systematic evaluation of variability in simulated ChIP-chip experiments Kevin_Encode
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.
Keywords: ChIP-chip

For data usage terms and conditions, please refer to and
Overall design 9 spike-in replicates and 9 genomic input control replicates
Web link
Contributor(s) Wei L
Citation(s) 18258921
BioProject PRJNA63447
Submission date Dec 12, 2007
Last update date Jun 28, 2012
Contact name Wei Li
Organization name Baylor College of Medicine
Street address one baylor plaza, MS BCM305
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
Platforms (1)
GPL6129 GeneChip ENCODEver2.0R Array - NCBI build 36
Samples (18)
GSM248996 Undiluted control rep1_B3
GSM248997 Undiluted control rep2_B2
GSM248998 Undiluted control rep3_B1
This SubSeries is part of SuperSeries:
GSE10114 Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

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
GSE9848_RAW.tar 716.2 Mb (http)(custom) TAR (of CEL) 11.7 Mb (ftp)(http) BAR 11.7 Mb (ftp)(http) BAR
Processed data are available on Series record

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