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Genomic and RNA Profiling Core Facility

Houston, Texas

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Genomic and RNA Profiling Core
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Affymetrix Promoter Arrays

DNA Protein Interaction 2 DNA Protein Interaction 2

Available Affymetrix Promoter arrays are the Human Promoter 1.0R and Mouse Promoter 1.0R arrays. These single arrays help researchers study DNA/protein interactions in over 25,000 promoters. The probes selected for these arrays are a subset of the probes on the Whole Genome Tiling arrays and are tiled at a resolution of approximately 35bp apart, measured from the center of adjacent 25-mer oligos.

Affymetrix provides a ChIP protocol for researchers to follow (optimization is required for each project due to variability in antibody binding). The IP workflow, which is completed by the researcher, consists of crosslinking DNA with the associated proteins, immunoprecipitating the DNA-protein complexes, reversing the crosslinks and purifying the DNA. GARP then fragments and labels the purified PCR products for hybridization onto the respective promoter arrays.

Starting Material Input Amount
Array Format dsDNA(PCR product) Minimum Concentration
Single-Array Format 7.5 µg 190 ng/µL

DNA fragmentation can be done using enzymatic methods, such as MNase or by physical shearing, such as Covaris, Bioruptor or tip probe sonicator. Get the Bioruptor User Guide.

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