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| == Platforms ==
| | The MIT BioMicro Center retains minimal support for Agilent and Affymetrix Microarrays. Assisted microarray serves are no longer available. The Agilent oven and microarray scanner are available to users who prepare their own arrays and remains under service contract. Our Affymetrix instrumentation is available for use at user's risk. |
| === Affymetrix ===
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| The MIT BioMicro Center preforms expression analysis using Affymetrix arrays. Our service includes: | |
| * Sample labeling and clean up using Affymentrix kits. ([http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf Product Manual])
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| * Array hybridization
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| * Data extraction and normalization
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| We currently use arrays designed for whole transcript expression and 3’ expression analysis arrays for eukaryotic and prokaryotic samples. We are exploring expanding our services to include SNP and Genotyping analyses. Please visit the [[BioMicroCenter:Ideas|IDEAS CENTER]] if you have input on the types of arrays you would like us to provide.
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| === Agilent ===
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| The MIT BioMicro Center hosts a high-throughput Agilent Microarray Scanner, which has ability to measure fluorescence from two dyes simultaneously facilitates differential gene expression studies. We are currently planning to reintroduce Agilent array hybridization services in 2009.
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| === Nimblegen ===
| | Please note that the BioMicro Center no longer supports printing of microarrays in house. 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 microarray printing, we encourage you to contact [http://jura.wi.mit.edu/genomecorewiki/index.php/Tom_Volkert Tom Volkert at the Whitehead Institute CGT]. |
| The BioMicro Center does not currently support the Nimblegen platform. We are currently discussing upgrading our Agilent Scanner to enable it to scan Nimblegen arrays as well. Anyone interested in using Nimblegen arrays should contact '''Stephen Bell'''.
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| | | === Agilent Data Analysis === |
| == Sample Submission Guidelines == | | Agilent Scanner is available to members of the MIT Community. We are currently running Feature extractor version 10.5. Please use [https://mit.ilabsolutions.com/sc/3381/ki-genomics-core-mit-biomicro-center/?tab=equipment iLabs] to book time on the instrument. |
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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 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
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| All submissions must be accompanied by a [[BioMicroCenter:Forms#Downloads | Affymetrix Submission Form]].
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| === Affymetrix Sample Concentrations ===
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| '''ARRAY''' '''Min.RNA''' '''CONCENTRATION''' '''NOTES'''
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| Prokaryote 10 ug >0.6 ug/ul
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| Euk. 3' Array 3 ug >0.3 ug/ul
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| [[3primeIVT|**New Kit**]] 0.1 ug http://www.affymetrix.com/products_services/reagents/specific/3_ivtexpresskit.affx
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| Euk. Exon Array 2 ug >0.5 ug/ul
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| '''January 2009'''
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| ** Affymetrix is retiring their old 3' Array kits in September. The [[3primeIVT|new kits]] are faster, require less starting material, and slightly less expensive (prices will be adjusted soon). Please indicate which type of kit you would like to use when submitting your sample.
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| Information about our evaluation of the new kits is [[3primeIVT|HERE]]
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| === Non-MIT Users ===
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| Please contact [[BioMicroCenter:People|Manlin Luo]] to arrange a drop off date and time. Samples on dry ice and chips at room temperature with a completed order form are shipped by overnight delivery to:
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| MIT BioMicro Center
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| Attention: Manlin Luo
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| 31 Ames Street, Building 68-316
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| Cambridge, MA 02139
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| == Protocol ==
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| <B><BIG>NEW!</BIG></B>
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| Affymetrix is switching their labeling kits to a new kit called [http://www.affymetrix.com/products_services/reagents/specific/3_ivtexpresskit.affx 3'IVT Express]<br>
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| Information about the new kit can be found [[3primeIVT|HERE]]
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| == Analysis and Data Retrieval ==
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| === Affymetrix Data Analysis ===
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| BioMicro Center will perform the initial data extraction of your samples using Affymetrix GCOS V.1.4. Affymetrix data is scaled to a average intensity of 500 per chip. Six files for each sample will be sent back to the user:
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| * .exp: Experiment information file
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| * .dat: The image of the scanned probe array.
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| * .cel: Cell Intensity File derived from .dat file.
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| * .chp: Output file generated from the analysis of a probe array.
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| * .rpt: Report File generated.
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| * .txt: Text File is the same information as the .chp file in text format.
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| Additional data analysis help is available on a case by case basis. Please contact [[BioMicroCenter:People|Stuart Levine]] if you need additional help with your analysis.
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| === Data Transfer ===
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| 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.
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| The data will be placed on our server and can be downloaded by secure FTP or SSH.
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| SSH can be downloaded from: ftp://metalab.unc.edu/pub/packages/security/ssh/SSHSecureShellClient-3.2.9.exe
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| Your user name and password will be included in the email. To obtain your data, enter the following in your client:
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| Host: bmc-150.mit.edu
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| user: provided in email
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| Password: provided in email
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| Please contact [[BioMicroCenter:People|Stephen Goldman]] if you have difficulty obtaining your data.
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| == Pricing ==
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| Prices for sample processing do not include cost of arrays
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| === [[BioMicroCenter:MicroArrays|AFFYMETRIX ARRAYS]] ===
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| Affymetrix processing prices '''do not''' include the cost of the array. In order to be sure we have arrays on hand, we encourage users to contact us several days in advance of submitting samples.
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| '''ITEM''' '''[[CoreDeps|CORE LAB]]''' '''MIT''' '''NON-MIT''' '''unit''' '''NOTES'''
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| Affy Expression Processing
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| Standard $260 $430 $645 per array *kit will be retired Sep.2009
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| Affy Exon Processing $300 $535 $800 per array
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| Common Affymetrix Arrays (in stock):
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| Human U133 Plus 2.0 $400
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| Human U133A 2.0 $250
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| Human Exon 1.0 ST $400
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| Mouse 430 2.0 $400
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| Mouse 430A 2.0 $250
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| Mouse Exon 1.0 ST $400
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| Yeast 2.0 $175
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| Full Price List: [[Media:Affy_Arrays_081218.pdf| Affymetrix Prices]]
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| >> Price of 3' Expression arrays will be decreasing in early 2009 to reflect changes in the hybridization protocol.
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| === AGILENT SCANNER ===
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| Agilent Scanner is available to members of the MIT Community without charge. If you are the first time user, contact [[BioMicroCenter:People|Stephen Goldman]] to set up a bionet account for your data storage. For questions about equipment, contact [[BioMicroCenter:People|Manlin Luo]]
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| After you have completed your scan, please make sure to sign the scanner record form, which is near the equipment and to remove your files from the computer. CD-Rs are available if needed.
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| === [[2100BioAnalyzer|AGILENT BIOANALYZER]] ===
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| '''ITEM''' '''[[CoreDeps|CORE LAB]]''' '''MIT''' '''NON-MIT''' '''unit''' '''NOTES'''
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| RNA $10 $10 $15 per sample
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