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| Status |
Public on Feb 01, 2008 |
| Title |
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets |
| Project |
ENCODE
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| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
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| 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.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
This SuperSeries is composed of the SubSeries listed below.
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| Overall design |
Refer to individual Series
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| Web link |
http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html
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| Citation(s) |
18258921 |
| BioProject |
PRJNA63447 |
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| Submission date |
Jan 09, 2008 |
| Last update date |
Dec 28, 2012 |
| Contact name |
Jason D Lieb |
| E-mail(s) |
jlieb@bio.unc.edu
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| Phone |
(919) 843-3228
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| Fax |
(919) 962-1625
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| URL |
http://www.bio.unc.edu/faculty/lieb/labpages/home.shtml
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| Organization name |
University of North Carolina at Chapel Hill
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| Department |
Department of Biology
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| Street address |
CB# 3280, 202 Fordham Hall
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-3280 |
| Country |
USA |
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| Platforms (6)
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| GPL2131 |
Nimblegen ENCODE Array |
| GPL3980 |
UC Davis Human ENCODE array |
| GPL4559 |
ENCODE NimbleGen hg17 tiling array |
| GPL6129 |
GeneChip ENCODEver2.0R Array - NCBI build 36 |
| GPL6189 |
Agilent 244k ENCODE custom tiling array |
| GPL6264 |
Homo Sapiens ENCODE 244k Array |
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| Samples (47)
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| 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) |
| GSM245949 |
Spike-in sample technical replicate 1 |
| GSM245950 |
Spike-in sample technical replicate 2 |
| GSM245951 |
Spike-in sample technical replicate 3, dye swap |
| GSM248654 |
Slide 1 |
| GSM248657 |
Slide 2 |
| GSM248666 |
Slide 3 |
| GSM248996 |
Undiluted control rep1_B3 |
| GSM248997 |
Undiluted control rep2_B2 |
| GSM248998 |
Undiluted control rep3_B1 |
| GSM248999 |
Undiluted spike-in rep1_B1 |
| GSM249000 |
Undiluted spike-in rep2_B2 |
| GSM249001 |
Undiluted spike-in rep3_B3 |
| GSM249002 |
Undiluted control rep1_B1_T1 |
| GSM249003 |
Undiluted control rep2_B2_T1 |
| GSM249004 |
Undiluted control rep3_B3_T1 |
| GSM249005 |
Undiluted spike-in rep1_B1_T1 |
| GSM249006 |
Undiluted spike-in rep2_B2_T1 |
| GSM249007 |
Undiluted spike-in rep3_B3_T1 |
| GSM249008 |
Amplified spike-in rep1_B1_T1 |
| GSM249009 |
Amplified spike-in rep2_B1_T1 |
| GSM249010 |
Amplified spike-in rep3_B1_T1 |
| GSM249011 |
Amplified control rep1_B1_T1 |
| GSM249012 |
Amplified control rep2_B1_T1 |
| GSM249013 |
Amplified control rep3_B1_T1 |
| GSM249014 |
Spike-in rep1 |
| GSM249015 |
Spike-in rep2 |
| GSM249016 |
Spike-in rep3 |
| GSM249017 |
Control rep1 |
| GSM249018 |
Control rep2 |
| GSM249019 |
Control rep3 |
| GSM252509 |
Slide 4 |
| GSM252780 |
ENCODE Spike-In, Yale Group Sample 1 |
| GSM252781 |
ENCODE Spike-In, Yale Group Sample 2 |
| GSM252782 |
ENCODE Spike-In, Yale Group Sample 3 |
| GSM254805 |
ENCODE spikein competition, amplified Sample, NimbleGen array 92181 |
| GSM254806 |
ENCODE spikein competition, amplified sample, rep 2of3, NimbleGen array 92303 |
| GSM254807 |
ENCODE spikein competition, amplified sample, NimbleGen array 96391 |
| GSM254930 |
ENCODE spikein competition, nonamplified sample, NimbleGen array 89832 |
| GSM254971 |
ENCODE spikein competition, nonamplified sample, NimbleGen array 89834 |
| GSM254972 |
ENCODE spikein competition, nonamplified sample, NimbleGen array 89840 |
| GSM254973 |
ENCODE spikein competition, nonamplified sample, NimbleGen array 96403 |
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| This SuperSeries is composed of the following SubSeries:
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| 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 |
| GSE9849 |
Systematic evaluation of variability in simulated ChIP-chip experiments Myles_Encode |
| GSE10004 |
ENCODE Spike-In, Yale Group |
| GSE10076 |
ENCODE spikein, amplified DNA samples, NimbleGen arrays |
| GSE10090 |
ENCODE spikein, nonamplified DNA samples, NimbleGen arrays |
| GSE10112 |
Systematic evaluation of variability in simulated ChIP-chip experiments |
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| 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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