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BioMicroCenter:Microarrays: Difference between revisions
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→Agilent vs. Affymetrix
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[http://www.affymetrix.com AFFYMETRIX] arrays are very high density arrays of 25mer oligonucleotides built by lithography. An Affymetrix probeset is composed of numerous neighboring perfect match and mismatch probes that are combined and used in the calculation of intensity and relative expression. Affymetrix arrays are the most common arrays used in genomics right now and have a rich bioinformatic architecture that allows for a large number of analyses. While expression arrays are the most common, Affymetrix also creates arrays for SNP calling and ChIP-chip. Affymetrix expression arrays come in two flavors: 3' and exon. 3' arrays use oligo dT priming while exon arrays amplify from the whole RNA using random primers. Affymetrix arrays are one-color arrays and use biotinylated nucleotides in the cRNA/cDNA to recruit HRP-peroxidase to the probes. Affymetrix arrays come as single arrays from a broad list of species. The BioMicro Center has a hybridization oven, two 450 fluidics devices and a 7G scanner for handling Affymetrix arrays. | [http://www.affymetrix.com AFFYMETRIX] arrays are very high density arrays of 25mer oligonucleotides built by lithography. An Affymetrix probeset is composed of numerous neighboring perfect match and mismatch probes that are combined and used in the calculation of intensity and relative expression. Affymetrix arrays are the most common arrays used in genomics right now and have a rich bioinformatic architecture that allows for a large number of analyses. While expression arrays are the most common, Affymetrix also creates arrays for SNP calling and ChIP-chip. Affymetrix expression arrays come in two flavors: 3' and exon. 3' arrays use oligo dT priming while exon arrays amplify from the whole RNA using random primers. Affymetrix arrays are one-color arrays and use biotinylated nucleotides in the cRNA/cDNA to recruit HRP-peroxidase to the probes. Affymetrix arrays come as single arrays from a broad list of species. The BioMicro Center has a hybridization oven, two 450 fluidics devices and a 7G scanner for handling Affymetrix arrays. | ||
[http://www.agilent.com AGILENT] arrays are lower density arrays then Affymetrix, but have much longer oligos (60mers) and are printed on glass slides using dot-matrix printing technologies. Because this method does not require the creation of metal plates, novel microarray designs cost no more then designs created by Agilent. Agilent arrays can be used for a variety of assays including gene expression, ChIP-chip, miRNA hybridization, and CGH. Our Agilent scanner was recently upgraded and can handle Agilent arrays of up to 1 million probes per slide (Donated by the Bell lab). Because of the lower probe density and the longer oligos used, each probe is evaluated separately. [[Image: | [http://www.agilent.com AGILENT] arrays are lower density arrays then Affymetrix, but have much longer oligos (60mers) and are printed on glass slides using dot-matrix printing technologies. Because this method does not require the creation of metal plates, novel microarray designs cost no more then designs created by Agilent. Agilent arrays can be used for a variety of assays including gene expression, ChIP-chip, miRNA hybridization, and CGH. Our Agilent scanner was recently upgraded and can handle Agilent arrays of up to 1 million probes per slide (Donated by the Bell lab). Because of the lower probe density and the longer oligos used, each probe is evaluated separately. [[Image:Multiple_arrays.jpg|right]] Each glass slide can contain multiple identical arrays (2, 4, or 8), reducing the cost per hybridization, often below the level of Affymetrix arrays. Typical mammalian expression arrays are in a 4x44k or 8x60k format where each slide contains four or eight identical arrays that are separable by a gasket slide. Agilent arrays can be hybridized either as one-color or two-color using Cy5 and Cy3 labeled cRNA/cDNA. We do not currently maintain a stock of Agilent arrays but do have a significant discount on the purchase of arrays. | ||
Please note that we have upgraded our Agilent DNA microarray scanner to the new scanning system enabled by SureScan High-Resolution Technology on April 2011. The new scanner is enable scanning of with 2, 3, 5 or 10 micron resolution glass slide microarrays; identifying weaker signals and preventing feature saturation; speeding up scan times; providing increased sensitivity and precision by dynamic autofocus, regardless of glass aberrations. That allows scanning of Agilent’s newest 1 million feature arrays. | Please note that we have upgraded our Agilent DNA microarray scanner to the new scanning system enabled by SureScan High-Resolution Technology on April 2011. The new scanner is enable scanning of with 2, 3, 5 or 10 micron resolution glass slide microarrays; identifying weaker signals and preventing feature saturation; speeding up scan times; providing increased sensitivity and precision by dynamic autofocus, regardless of glass aberrations. That allows scanning of Agilent’s newest 1 million feature arrays. | ||
