ChIP-on-chip Custom Arrays
ChIP-on-chip Custom Arrays
Jump to:
Featured Research Using This Product
Additional Resources
Product Details
Note: This is a review of the published article listed below. All information, quotes, figures, methods, and findings mentioned in this review are from that article, and are the property of its authors and/or the publication in which the article originally appeared.
Agilent’s custom ChIP-on-chip microarray sets for location analysis enable you to select genomic regions from any organism of interest for tiling at a desired resolution from Agilent- or customer-designed ChIP-on-chip probes. Whether you require whole genome, selected, or focused formats, Agilent’s SurePrint inkjet technology ensures high-precision feature placement through base-by-base synthesis and a robust QC process, resulting in superior quality microarrays. Design a single or a set of fully-customized microarrays, utilizing two-color labeling for enhanced sensitivity, accuracy, and reproducibility to identify weak- and infrequent-binding events. Available organism sources include Arabidopsis, C. elegans, Drosophila, human, mouse, yeast, zebrafish, S. pombe, and pseudomonas.
Wardle et al (2006) took advantage of Agilent’s custom ChIP-on-chip services to identify actively transcribed embryonic genes in zebrafish by designing a genomic microarray to identify DNA-protein interactions in the proximal promoter regions of over 11,000 zebrafish genes. The techniques employed by the group pave the way for studying genome-wide binding of regulatory factors during vertebrate embryogenesis. Further, the results demonstrate the feasibility of a genomic platform to study factor binding in zebrafish, enabling the characterization of transcriptional networks in the developing embryo on a genome-wide scale.
Figure 1. ChIP-chip method in zebrafish embryos.
(a) Design of promoter arrays: 60-mer oligonucleotides were designed against genomic sequence 1.5 kb upstream and 0.5 kb downstream of the annotated transcription start site of approximately 11,000 zebrafish genes. The resulting probes are arrayed onto two microarray slides. (b) ChIP-array protocol. (c) Examples of scatter plots obtained from one hybridization of immunoprecipitated DNA on one 2-slide proximal promoter microarray set. Log2 ratios for each labeled sample are plotted against each other. Enriched probes are seen above the diagonal. Control spots (zebrafish gene desert and Arabidopsis gene probes), shown in red, fall along the diagonal.
Figure 2. H3K4Me3 is enriched at the 5' end of ubiquitously expressed genes but not enriched at non-expressed genes.
(a) Examples of genes marked by H3K4Me3 showing a peak of enrichment at the 5' end of the gene. (b) Examples of non-expressed genes that are not marked by H3K4Me3. For (a) and (b) plots show unprocessed ChIP-enrichment ratios for all probes within a genomic region. The chromosomal position (based on Zv4 genome assembly annotation) and the transcription start site and direction of transcription for each gene are shown below each graph. The x-axes are not to scale.
Figure 3. H3K4Me3 is enriched at the 5' end of genes expressed in localized domains of the embryo.
Plots show unprocessed ChIP-enrichment ratios for all probes within a genomic region. The chromosomal position (based on Zv4 genome assembly annotation) and the transcription start site and direction of transcription for each gene are shown below each graph.
Original Research Paper:
Title: Zebrafish promoter microarrays identify actively transcribed embryonic genes.
Authors: Wardle FC, Odom DT, Bell GW, Yuan B, Danford TW, Wiellette EL, Herbolsheimer E, Sive HL, Young RA, Smith JC.
Journal: Genome Biol. 2006 Aug 4;7(8):R71.
More
Listen to Agilent researchers present current product information.
View available eSeminars
For detailed specifications and ordering information visit agilent.com