Editing BioMicroCenter:MicroArrays

{{BioMicroCenter}}

[[Image:Presentation7.jpg|right|300px]]
== Platforms ==
=== Affymetrix ===
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])
* Array hybridization 
* Data extraction and normalization 
 
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.

=== 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 [[BioMicroCenter:Forms#Downloads | 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
 [[BioMicroCenter:3primeIVT|**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 [[BioMicroCenter: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.

Information about our evaluation of the new kits is [[BioMicroCenter:3primeIVT|HERE]]

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

== Protocol ==

<B><BIG>NEW!</BIG></B>
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>

Information about the new kit can be found [[BioMicroCenter:3primeIVT|HERE]]


== Analysis and Data Retrieval ==

=== 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 [[BioMicroCenter:People|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 SFTP.
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 [mailto:bmc-data@mit.edu bmc-data@mit.edu] if you have difficulty obtaining your data.

== Pricing ==
Prices for sample processing do not include cost of arrays	

=== [[BioMicroCenter:MicroArrays|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'''                       '''[[CoreDeps|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 [[BioMicroCenter:People|Stephen Goldman]] to set up a bionet account for your data storage. For questions about equipment, contact [[BioMicroCenter:People|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.

=== [[BioMicroCenter:2100BioAnalyzer|AGILENT BIOANALYZER]] ===

   '''ITEM'''                       '''[[CoreDeps|CORE LAB]]'''       '''MIT'''      '''NON-MIT'''     '''unit'''          '''NOTES'''
   RNA                           $10         $10        $15      per sample

.

[[BioMicroCenter:MicroArrayTemp|NEW PAGE]]