ArticleNucleic acids research2008
Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 33 citations in OpenAlex.
- Inhibiting MYC binding to the E-box DNA motif by ME47 decreases tumour xenograft growth.Oncogene · 2017Article
- The long noncoding RNA XIAP-AS1 promotes XIAP transcription by XIAP-AS1 interacting with Sp1 in gastric cancer cells.PloS one · 2017Article
- MYC interaction with the tumor suppressive SWI/SNF complex member INI1 regulates transcription and cellular transformation.Cell cycle (Georgetown, Tex.) · 2016Article
- Sandcastle: software for revealing latent information in multiple experimental ChIP-chip datasets via a novel normalisation procedure.Scientific reports · 2015Article
- Knowledge Discovery and interactive Data Mining in Bioinformatics--State-of-the-Art, future challenges and research directions.BMC bioinformatics · 2014Article
- Identifying gene locus associations with promyelocytic leukemia nuclear bodies using immuno-TRAP.The Journal of cell biology · 2013Article
- Nanobody(R)-based chromatin immunoprecipitation/micro-array analysis for genome-wide identification of transcription factor DNA binding sites.Nucleic acids research · 2013Article
- Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations.PLoS computational biology · 2013Article
- Limitations and possibilities of low cell number ChIP-seq.BMC genomics · 2012Article
- Integrative computational biology for cancer research.Human genetics · 2011Review
- Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation.Genome research · 2010Article
- 3-methylcholanthrene induces differential recruitment of aryl hydrocarbon receptor to human promoters.Toxicological sciences : an official journal of the Society of Toxicology · 2010Article
- Time-dependent c-Myc transactomes mapped by Array-based nuclear run-on reveal transcriptional modules in human B cells.PloS one · 2010Article
- Mitogenic regulation of p27(Kip1) gene is mediated by AP-1 transcription factors.The Journal of biological chemistry · 2010Article
- Evaluation of linguistic features useful in extraction of interactions from PubMed; application to annotating known, high-throughput and predicted interactions in I2D.Bioinformatics (Oxford, England) · 2010Article
- Fast genomic muChIP-chip from 1,000 cells.Genome biology · 2009Article
- Overview of electrochemical DNA biosensors: new approaches to detect the expression of life.Sensors (Basel, Switzerland) · 2009Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput, microarray-based chromatin immunoprecipitation (ChIP-chip) technology allows in vivo elucidation of transcriptional networks. However this complex is not yet readily accessible, in part because its many parameters have not been systematically evaluated and optimized. We address this gap by systematically assessing experimental-design parameters including antibody purity, dye-bias, array-batch, inter-day hybridization bias, amplification method and choice of hybridization control. The combined performance of these optimized parameters shows a 90% validation rate in ChIP-chip analysis of Myc genomic binding in HL60 cells using two different microarray platforms. Increased sensitivity and decreased noise in ChIP-chip assays will enable wider use of this methodology to accurately and affordably elucidate transcriptional networks.
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