ChIP-on-chip Model Organism Arrays
ChIP-on-chip Model Organism Arrays
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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.
The Agilent platform offers a diverse selection of chromatin immunoprecipitation (ChIP)-on-chip microarrays, featuring ~244,000 targeted 60-mer oligonucleotide probes covering coding and non-coding sequences that span regions-of-interest. 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. Agilent’s ChIP-on-chip formats feature predesigned, high-resolution microarrays that utilize two-color labeling for greater sensitivity, accuracy, and reproducibility, enabling you to identify weak- and infrequent-binding events, while proprietary algorithms generate reliable data with fewer false positives. Available model organisms include Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, human, mouse, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Pseudomonas aeruginosa, and Danio rerio.
Use of model organism systems provides valuable insight into gene function and regulation. Information obtained with model organisms is helpful in characterizing homologous processes in human cells and diseases. ChIP-on-chip, also known as Location Analysis (LA), allows precise localization of where regulatory proteins are bound on genomic DNA By incorporating ChIP into a microarray format, binding events can be quickly identified across the entire genome.Wardle et al (2006) took advantage of Agilent’s ChIP-on-chip microarrays to identify actively transcribed zebrafish embryonic genes. They identified DNA-protein interactions in proximal promoter regions of over 11,000 zebrafish genes. The approach employed by the group paves the way for studying genome-wide binding of regulatory factors during vertebrate embryogenesis and development. Results validate the feasibility of using such a genomic platform to expedite assembly of genetic networks.
Figure 1. ChIP-chip method in zebrafish embryos.
A. Oligonucleotide probe design for genomic sequence 1.5 KB upstream and 0.5 KB downstream of annotated transcription start sites of ~11,000 zebrafish genes. Resulting probes were arrayed onto two microarray slides. B. Basic ChIP-on-chip protocol utilized. C. Examples of scatter plots obtained from immunoprecipitated DNA hybridizations on one two-slide proximal promoter microarray set. Log2 ratios for each labeled sample are plotted against each other. Enriched probes appear above the diagonal. Control spots (Danio rerio gene desert and Arabidopsis thaliana gene probes) are shown in red and fall along the diagonal.
Figure 2. Trimethylated K4 Histone H3 (H3K4Me3)-enriched binding profiles
A. Gene examples marked by H3K4Me3 showing a peak of enrichment at the 5'end. B. Non-expressed gene examples that are not marked by H3K4Me3. Both subsets show unprocessed ChIP-on-chip enrichment ratios for all probes within a genomic region. The chromosomal position (based on the Zv4 genome assembly annotation) and the transcription start site and direction of transcription for each gene are noted below each graph. X-axes are not to scale.
Figure 3. Trimethylated K4 Histone H3 (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 the Zv4 genome assembly annotation) and the transcription start site and direction of transcription for each gene are noted 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.
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Arabidopsis Whole Genome: explore gene regulation in embryonic and adult development as well as signaling networks using probes tiled across the entire Arabidopsis genome with 212 nt average spacing on a 244K array set
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C. elegans Whole Genome: a valuable model system that can provide developmental insights based on gene regulation using probes tiled across the whole C. elegans genome with 182 nt average spacing on a 244K array set
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Drosophila Whole Genome: wild-type and mutant strains of Drosophila provide information on genetics, embryonic and adult development, and signaling networks as a model for vertebrate systems, using probes tiled across the entire genome with 233 nt average spacing on a 244K array set
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Yeast Whole Genome 4 x 44K: specifically designed for streamlined location analysis of yeast DNA binding proteins with roughly 85% of the non-repetitive portion of the yeast genome and an average probe spatial resolution of 290 nt on a 44K array. 4 arrays per slide.
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Yeast Whole Genome 244 K: designed to perform higher resolution applications, such as nucleosome tiling, with 50 nt resolution of the yeast genome on an expanded 244K array
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Zebrafish Expanded Promoter: collaboratively designed with researchers from the Whitehead Institute for research related to vertebrate development using an expanded promoter 9-array set with probes that cover -9 KB to +3 KB from transcriptional start sites of 11,000 genes on a 44K array
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Zebrafish Proximal Promoter: also collaboratively designed with researchers from the Whitehead Institute for research related to vertebrate development using a proximal promoter 2-array set that contains probes that cover -1.5 KB to +.5 KB from transcriptional start sites of 11,000 genes on a 44K array
For detailed specifications and ordering information visit agilent.com