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BioMicroCenter:Microarrays: Difference between revisions
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[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. 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. | [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. 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 | 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. | ||
As of July 2011, on a per sample basis, Agilent arrays | As of July 2011, on a per sample basis, Agilent arrays cost considerably less then Affymetrix Genechips (under $400 per array), but must be processed as whole slides. | ||
Please note that the BioMicro Center no longer supports self printed arrays. Custom oligonuclotide arrays are available from Agilent at the same cost as their commercial arrays using their [http://www.chem.agilent.com/en-US/products/instruments/dnamicroarrays/pages/gp50660.aspx eArray system] (we can [[BioMicroCenter:Computing#BioInformatics_Services|help you]] through the process of designing arrays). For anyone requiring self printed arrays, we encourage you to contact [http://jura.wi.mit.edu/genomecorewiki/index.php/Tom_Volkert Tom Volkert at the Whitehead Institute CGT]. | Please note that the BioMicro Center no longer supports self printed arrays. Custom oligonuclotide arrays are available from Agilent at the same cost as their commercial arrays using their [http://www.chem.agilent.com/en-US/products/instruments/dnamicroarrays/pages/gp50660.aspx eArray system] (we can [[BioMicroCenter:Computing#BioInformatics_Services|help you]] through the process of designing arrays). For anyone requiring self printed arrays, we encourage you to contact [http://jura.wi.mit.edu/genomecorewiki/index.php/Tom_Volkert Tom Volkert at the Whitehead Institute CGT]. | ||
