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BioMicroCenter:Microarrays: Difference between revisions
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== BioMicro Center Services == | == BioMicro Center Services == | ||
We are currently set up to primarily handle expression analysis. Our service includes: | We are currently set up to primarily handle expression analysis. Our service includes: | ||
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* Array Hybridization | * Array Hybridization | ||
* Data extraction and normalization | * Data extraction and normalization | ||
We also have discounts with different vendors and can help you purchase your arrays. | We also have discounts with different vendors and can help you purchase your arrays. | ||
<br> | <br> | ||
=== SAMPLE TYPES === | === SAMPLE TYPES === | ||
The BioMicro Center has extensive experience handling samples for expression analysis. | The BioMicro Center has extensive experience handling samples for expression analysis. | ||
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| Affymetrix | | Affymetrix | ||
| labeling using NuGEN for Affy arrays | | labeling using NuGEN for Affy arrays | ||
|- | |||
| CGH | |||
| 3ug | |||
| 6 μL | |||
| Agilent | |||
| labeling using Agilent's CGH kit | |||
|- | |- | ||
| small RNA | | small RNA | ||
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We encourage researchers to contact us several days in advance of sample submission to allow us lead time to purchase any specialized Affymetrix or Agilent arrays. While we keep a few arrays in stock, most arrays are ordered on an as needed basis. A list of some of the available arrays and their prices can be found [[Media:Affy_Arrays_081218.pdf| in this file]]. Information about Affymetrix arrays is available at http://www.affymetrix.com/products_services/index.affx | We encourage researchers to contact us several days in advance of sample submission to allow us lead time to purchase any specialized Affymetrix or Agilent arrays. While we keep a few arrays in stock, most arrays are ordered on an as needed basis. A list of some of the available arrays and their prices can be found [[Media:Affy_Arrays_081218.pdf| in this file]]. Information about Affymetrix arrays is available at http://www.affymetrix.com/products_services/index.affx | ||
All submissions must be accompanied by a [[BioMicroCenter:Forms#Downloads | Affymetrix Submission Form]]. | All submissions must be accompanied by a [[BioMicroCenter:Forms#Downloads | Affymetrix or Agilent Submission Form]]. | ||
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=== TURN AROUND === | === TURN AROUND === | ||
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=== | == ARRAY SELECTION == | ||
==== [[BioMicroCenter:Pricing|PRICES]] | There are several considerations to take into account in selecting your microarray. We provide support for multiple array platforms from two different manufacturers (Agilent and Affymetrix). Additionally, multiple labeling methods are available for each platform. Each labeling method has different sample requirements and multiple labeling methods should NOT be combined in doing post-hybridization analysis. | ||
=== Agilent vs. Affymetrix === | |||
Affymetrix arrays are very high density arrays of 30mer 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. 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. | |||
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. Our Agilent scanner can handle Agilent arrays of up to 250k probes per slide. 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 format where each slide contains four identical arrays that are seperable by a gasket slide. Agilent arrays can be hybridized either as one-color or two-color using Cy5 and Cy3 labeled cRNA/cDNA. | |||
=== Labeling Methods === | |||
== LINKS == | |||
=== [[BioMicroCenter:Pricing|PRICES]] === | |||
=== [[BioMicroCenter:FAQ#NON_MIT_USERS|Information for non-MIT labs]] === | |||
=== [[BioMicroCenter:FAQ#HOW_DO_I_GET_MY_DATA|Obtaining your results]] === | |||
You will be notified by email that your data is ready. At that time please pick up any leftover samples and arrays belonging to you. Samples will be held at the facility at -80C for 60 days after your data is generated. Information on downloading your data is in the link above. | You will be notified by email that your data is ready. At that time please pick up any leftover samples and arrays belonging to you. Samples will be held at the facility at -80C for 60 days after your data is generated. Information on downloading your data is in the link above. | ||
