BioMicroCenter:MicroArrays

Affymetrix
The MIT BioMicro Center preforms expression analysis using Affymetrix arrays. Our service includes: 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 IDEAS CENTER if you have input on the types of arrays you would like us to provide.
 * Sample labeling and clean up using Affymentrix kits. (Product Manual)
 * Array hybridization
 * Data extraction and normalization

Agilent
The MIT BioMicro Center hosts a high-throughput Agilent Microarray Scanner, which has the ability to measure fluorescence from two dyes simultaneously facilitating differential gene expression studies. We have just reintroduced Agilent array hybridization services as of October 2009.

Nimblegen
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.

Sample Submission Guidelines
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

All submissions must be accompanied by a Affymetrix Submission Form.

Affymetrix Sample Concentrations
ARRAY              Min.RNA   CONCENTRATION     NOTES Prokaryote         10 ug     >0.6 ug/ul Euk. 3' Array       3 ug     >0.3 ug/ul **New Kit**       0.1 ug                     http://www.affymetrix.com/products_services/reagents/specific/3_ivtexpresskit.affx Euk. Exon Array     2 ug     >0.5 ug/ul

January 2009
 * Affymetrix is retiring their old 3' Array kits in September. The 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.

Information about our evaluation of the new kits is HERE

Non-MIT Users
Please contact 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: MIT BioMicro Center Attention: Manlin Luo 31 Ames Street, Building 68-316 Cambridge, MA 02139

Protocol
NEW! Affymetrix is switching their labeling kits to a new kit called 3'IVT Express

Information about the new kit can be found HERE

Affymetrix Data Analysis
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:


 * .exp: Experiment information file
 * .dat: The image of the scanned probe array.
 * .cel: Cell Intensity File derived from .dat file.
 * .chp: Output file generated from the analysis of a probe array.
 * .rpt: Report File generated.
 * .txt: Text File is the same information as the .chp file in text format.

Additional data analysis help is available on a case by case basis. Please contact Stuart Levine if you need additional help with your analysis.

Data Transfer
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.

The data will be placed on our server and can be downloaded by secure FTP or SSH. SSH can be downloaded from: ftp://metalab.unc.edu/pub/packages/security/ssh/SSHSecureShellClient-3.2.9.exe Your user name and password will be included in the email. To obtain your data, enter the following in your client:

Host:      bmc-150.mit.edu user:      provided in email Password:  provided in email

Please contact Stephen Goldman if you have difficulty obtaining your data.

Pricing
Prices for sample processing do not include cost of arrays

AFFYMETRIX ARRAYS
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.

ITEM                      CORE LAB       MIT      NON-MIT     unit          NOTES Affy Expression Processing Standard                   $260        $430       $645      per array    *kit will be retired Sep.2009 Affy Exon Processing          $300        $535       $800      per array Common Affymetrix Arrays (in stock): Human U133 Plus 2.0        $400 Human U133A 2.0            $250 Human Exon 1.0 ST          $400 Mouse 430 2.0              $400 Mouse 430A 2.0             $250 Mouse Exon 1.0 ST          $400 Yeast 2.0                  $175 Full Price List:           [[Media:Affy_Arrays_081218.pdf| Affymetrix Prices]]

>> Price of 3' Expression arrays will be decreasing in early 2009 to reflect changes in the hybridization protocol.

AGILENT SCANNER
Agilent Scanner is available to members of the MIT Community at a charge of $50 per slide. We hope to reduce this number if usage allows us to. If you are the first time user, contact Stephen Goldman to set up a bionet account for your data storage. For questions about equipment, contact Manlin Luo

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.

AGILENT BIOANALYZER
ITEM                      CORE LAB       MIT      NON-MIT     unit          NOTES RNA                          $10         $10        $15      per sample

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