Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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ENCODE Spike-In, Yale Group


ABSTRACT: Simulated ChIP DNA labeled by random priming with Klenow; Samples were "Undiluted" and not amplified prior to labeling. Keywords: other For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Systematic analysis of a simulated ChIP-chip experiment

ORGANISM(S): Homo sapiens

SUBMITTER: Guoneng Zhong 

PROVIDER: E-GEOD-10004 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.

Johnson David S DS   Li Wei W   Gordon D Benjamin DB   Bhattacharjee Arindam A   Curry Bo B   Ghosh Jayati J   Brizuela Leonardo L   Carroll Jason S JS   Brown Myles M   Flicek Paul P   Koch Christoph M CM   Dunham Ian I   Bieda Mark M   Xu Xiaoqin X   Farnham Peggy J PJ   Kapranov Philipp P   Nix David A DA   Gingeras Thomas R TR   Zhang Xinmin X   Holster Heather H   Jiang Nan N   Green Roland D RD   Song Jun S JS   McCuine Scott A SA   Anton Elizabeth E   Nguyen Loan L   Trinklein Nathan D ND   Ye Zhen Z   Ching Keith K   Hawkins David D   Ren Bing B   Scacheri Peter C PC   Rozowsky Joel J   Karpikov Alexander A   Euskirchen Ghia G   Weissman Sherman S   Gerstein Mark M   Snyder Michael M   Yang Annie A   Moqtaderi Zarmik Z   Hirsch Heather H   Shulha Hennady P HP   Fu Yutao Y   Weng Zhiping Z   Struhl Kevin K   Myers Richard M RM   Lieb Jason D JD   Liu X Shirley XS  

Genome research 20080207 3


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 eigh  ...[more]

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