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| Status |
Public on Dec 31, 2008 |
| Title |
Systematic evaluation of variability in simulated ChIP-chip experiments |
| Project |
ENCODE
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| 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 http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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| |
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| Overall design |
See manuscript for details
|
| Web link |
http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html
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| |
|
| Contributor(s) |
Ye Z, Ching K, Ren B |
| Citation(s) |
18258921 |
| BioProject |
PRJNA63447 |
| |
| Submission date |
Jan 09, 2008 |
| Last update date |
Jun 28, 2012 |
| Contact name |
Bing Ren |
| E-mail(s) |
biren@ucsd.edu
|
| Organization name |
Ludwig Institute for Cancer Research
|
| Department |
Department of Cellular and Molecular Medicine
|
| Lab |
Laboratory of Gene Regulation
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093-0653 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL4559 |
ENCODE NimbleGen hg17 tiling array |
|
| Samples (6)
|
| 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) |
| GSM245284 |
No Ab Spike in DNA sample undiluted ENCODE NimbleGen hg17 tiling array (90991) |
| GSM245285 |
No Ab Spike in DNA sample undiluted ENCODE NimbleGen hg17 tiling array (91991) |
| GSM245286 |
No Ab Spike in DNA sample diluted ENCODE NimbleGen hg17 tiling array (92003) |
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| This SubSeries is part of SuperSeries: |
| GSE10114 |
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets |
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