BioMicroCenter:Microarrays

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[[Image:Presentation7.jpg|right|300px]]
[[Image:Presentation7.jpg|right|300px]]
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== Platforms ==
+
Microarray technology is the principle service offered by the MIT BioMicro Center. BMC has extensive experience with several different types of samples and platforms. Microarray labeling and hybridization are typically preformed by BioMicro Center technicians, however our scanners, hybridization ovens and wash stations are available by request.  
-
=== 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 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.
+
-
 
+
-
=== 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]].  
+
== BioMicro Center Services ==
 +
We are currently set up to primarily handle expression analysis. Our service include:
-
=== Affymetrix Sample Concentrations ===
+
* Evaluation of sample quality using the [[BioMicroCenter:2100BioAnalyzer|Agilent BioAnalyzer 2100]]
-
'''ARRAY'''              '''Min.RNA'''  '''CONCENTRATION'''    '''NOTES'''
+
* Sample labeling and clean up.
-
Prokaryote          10 ug    >0.6 ug/ul
+
* Array Hybridization.
-
Euk. 3' Array        3 ug    >0.3 ug/ul
+
* Data extraction and normalization.
-
[[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
+
 +
We also have discounts with different vendors and can help you purchase your arrays.
 +
<br>
 +
=== SAMPLE TYPES ===
 +
The BioMicro Center has extensive experience handling samples for expression analysis.
-
'''January 2009'''
+
{|border=1
-
** 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.
+
|-
 +
! Eukaryote
 +
! Min.RNA
 +
! Min.Vol.
 +
! Notes
 +
|-
 +
| Prokaryote
 +
| 1 μg
 +
| 6 μL
 +
| labeling using [http://www.ambion.com/catalog/ProdGrp.html?fkProdGrp=339 Ambion] for Affy arrays
 +
|-
 +
| 3' Array (std)
 +
| 100 ng
 +
| 6 μL
 +
| labeling using NuGEN for Affy arrays.  
 +
|-
 +
| Exon Array
 +
| 100 ng
 +
| 6 μL
 +
| labeling using NuGEN for Affy arrays
 +
|-
 +
| small RNA
 +
| N/A
 +
| N/A
 +
|BMC recommends the use of multiplexed [[BioMicroCenter:Sequencing|Illumina sequencing]] for small RNA samples
 +
|}
 +
<br>
 +
=== SAMPLE SUBMISSION ===
-
Information about our evaluation of the new kits is [[BioMicroCenter:3primeIVT|HERE]]
+
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
-
=== Non-MIT Users ===
+
All submissions must be accompanied by a [[BioMicroCenter:Forms#Downloads | Affymetrix Submission Form]].
 +
<br>
 +
=== TURN AROUND ===
 +
The BioMicro Center will turn around your samples as quickly as possible. We are currently exploring methods of increasing our sample throughput to reduce turn around time. Average turn around time is currently 2-3 weeks.
 +
<br>
 +
=== 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:
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:
Line 44: Line 61:
   31 Ames Street, Building 68-316
   31 Ames Street, Building 68-316
   Cambridge, MA 02139
   Cambridge, MA 02139
 +
<br>
 +
=== [[BioMicroCenter:Prices|PRICES]] ===
 +
Please note that 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.
-
== Protocol ==
+
{| border=1  style="text-align:center"
 +
! ITEM
 +
! style="width:100px"|[[CoreDeps|CORE LAB]]
 +
! style="width:100px"| MIT
 +
! style="width:100px"| NON-MIT
 +
! style="width:100px"| unit
 +
|-
 +
| Affy 3' Processing || $260 || $430 || $645 || per array
 +
|- 
 +
| Affy Exon Processing || $300 || $535 || $800 || per array
 +
|-
 +
| Affy Prokaryote || $260 || $430 || $645 || per array
 +
|-
 +
| Agilent Arrays || (inquire) || || ||
 +
|}
-
<B><BIG>NEW!</BIG></B>
+
Common Affymetrix Arrays (some in stock):
-
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>
+
* Human U133 Plus 2.0 / Mouse 430 2.0 - '''$400'''
 +
* Human U133A 2.0 / Mouse 430A 2.0 - '''$250'''
 +
* Human / Mouse Exon 1.0 ST - '''$400'''
 +
* Yeast 2.0 - '''$175'''
 +
Full Price List: [[Media:Affy_Arrays_081218.pdf| Affymetrix Prices]]
-
Information about the new kit can be found [[BioMicroCenter:3primeIVT|HERE]]
+
** Please note: Processing prices will be changing on July 1, 2009 **
 +
== Platforms ==
 +
 +
The BioMicro Center currently processes two types of Arrays:
 +
 +
* [http://www.affymetrix.com AFFYMETRIX] - Affymetrix offers one color arrays for a variety of assays including expression, ChIP-chip, and SNP analysis. We routinely use Affymtrix arrays for the quantification of 3' ends and whole transcripts (exon arrays) from both eukaryotes and prokaryotes. The BioMicro Center has a hybridization oven, two 450 fluidics devices and a 7G scanner for handling Affymetrix arrays. As part of our effort to control costs, the BioMicro Center is part of the Core Lab program, which lowers our annual maintenance contract and we maintain a number of standard array types in stock.
 +
 +
* [http://www.agilent.com AGILENT] - Agilent offers two-color arrays for a variety of assays including gene expression, ChIP-chip, miRNA hybridization, and CGH. The MIT BioMicro Center hosts a hybridization oven and a high-throughput Agilent Microarray Scanner donated by the Bell lab. We do not currently maintain a stock of Agilent arrays but do have a significant discount on the purchase of arrays.
 +
 +
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].
 +
 +
== Technology Updates ==
 +
 +
=== Labeling Kits ===
 +
[[Image:BMC_NugenKit.png|right]]
 +
Affymetrix is retiring their old 3' Array kits in September 2009. In response, BMC has been evaluating new technologies. The newer kits are faster and require less starting material. We have selected the NuGEN technology as the primary labeling method we will be using going forward for eukaryotic arrays becuase of their ease and the modularity of their system that allows us to combine the processing of Affymetrix 3', Affymetrix Exon, and Agilent arrays. Information on the evaluation can be found '''[[BioMicroCenter:3primeIVT|HERE]].'''. We DO NOT RECOMMEND mixing labeling types withing an experiment as we observed large differences between the absolute intensitites of signals between labeling methods. Arrays can still be hybridized using the Affymetrix 3'IVT, Affymetrix Exon and old Affymetrix 3' array by request (please ask for pricing).
 +
 +
We have also switched our prokaryotic labeling system from the Affymetrix system to one developed by [http://www.ambion.com/catalog/ProdGrp.html?fkProdGrp=339 Ambion]. The Ambion sytem requires significantly less input RNA and has a more streamlined protocol. The Affymetrix labeling system is still available by request.
 +
 +
=== Small Cell Numbers ===
 +
 +
NuGEN has recently developed kits that allow the analysis of very [http://www.nugeninc.com/nugen/index.cfm/products/amplification-systems/wt-ovation-pico/ small amounts of pruified RNA (100pg)] or even [http://www.nugeninc.com/nugen/index.cfm/products/amplification-systems/wt-ovation-one-direct/ single cells]. Please contact [[BioMicroCenter:People|Stuart Levine]] if you are interested in trying out these technologies.
== Analysis and Data Retrieval ==
== Analysis and Data Retrieval ==
Line 57: Line 116:
=== Affymetrix Data Analysis ===
=== 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:
+
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 provided to the user:
* .exp: Experiment information file  
* .exp: Experiment information file  
Line 67: Line 126:
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.
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.
 +
 +
=== Agilent Data Analysis ===
 +
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]]
 +
 +
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.
 +
=== Data Transfer ===
=== Data Transfer ===
Line 80: Line 145:
   Password:  provided in email
   Password:  provided in email
-
Please contact [[BioMicroCenter:People|Stephen Goldman]] if you have difficulty obtaining your data.
+
Please contact [[BioMicroCenter:People|Stephen Goldman]] 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'''                      '''[[BioMicroCenter: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 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]]
+
-
 
+
-
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'''                      '''[[BioMicroCenter:CoreDeps|CORE LAB]]'''      '''MIT'''      '''NON-MIT'''    '''unit'''          '''NOTES'''
+
-
  RNA                          $10        $10        $15      per sample
+
-
 
+
-
.
+

Revision as of 21:11, 3 May 2009

Image:BioMicroCenter-header6.jpg

Microarray technology is the principle service offered by the MIT BioMicro Center. BMC has extensive experience with several different types of samples and platforms. Microarray labeling and hybridization are typically preformed by BioMicro Center technicians, however our scanners, hybridization ovens and wash stations are available by request.

Contents

BioMicro Center Services

We are currently set up to primarily handle expression analysis. Our service include:

  • Evaluation of sample quality using the Agilent BioAnalyzer 2100
  • Sample labeling and clean up.
  • Array Hybridization.
  • Data extraction and normalization.

We also have discounts with different vendors and can help you purchase your arrays.

SAMPLE TYPES

The BioMicro Center has extensive experience handling samples for expression analysis.

Eukaryote Min.RNA Min.Vol. Notes
Prokaryote 1 μg 6 μL labeling using Ambion for Affy arrays
3' Array (std) 100 ng 6 μL labeling using NuGEN for Affy arrays.
Exon Array 100 ng 6 μL labeling using NuGEN for Affy arrays
small RNA N/A N/A BMC recommends the use of multiplexed Illumina sequencing for small RNA samples


SAMPLE SUBMISSION

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 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.

TURN AROUND

The BioMicro Center will turn around your samples as quickly as possible. We are currently exploring methods of increasing our sample throughput to reduce turn around time. Average turn around time is currently 2-3 weeks.

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


PRICES

Please note that 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
Affy 3' Processing $260 $430 $645 per array
Affy Exon Processing $300 $535 $800 per array
Affy Prokaryote $260 $430 $645 per array
Agilent Arrays (inquire)

Common Affymetrix Arrays (some in stock):

  • Human U133 Plus 2.0 / Mouse 430 2.0 - $400
  • Human U133A 2.0 / Mouse 430A 2.0 - $250
  • Human / Mouse Exon 1.0 ST - $400
  • Yeast 2.0 - $175

Full Price List: Affymetrix Prices

** Please note: Processing prices will be changing on July 1, 2009 **

Platforms

The BioMicro Center currently processes two types of Arrays:

  • AFFYMETRIX - Affymetrix offers one color arrays for a variety of assays including expression, ChIP-chip, and SNP analysis. We routinely use Affymtrix arrays for the quantification of 3' ends and whole transcripts (exon arrays) from both eukaryotes and prokaryotes. The BioMicro Center has a hybridization oven, two 450 fluidics devices and a 7G scanner for handling Affymetrix arrays. As part of our effort to control costs, the BioMicro Center is part of the Core Lab program, which lowers our annual maintenance contract and we maintain a number of standard array types in stock.
  • AGILENT - Agilent offers two-color arrays for a variety of assays including gene expression, ChIP-chip, miRNA hybridization, and CGH. The MIT BioMicro Center hosts a hybridization oven and a high-throughput Agilent Microarray Scanner donated by the Bell lab. We do not currently maintain a stock of Agilent arrays but do have a significant discount on the purchase of arrays.

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 eArray system (we can help you through the process of designing arrays). For anyone requiring self printed arrays, we encourage you to contact Tom Volkert at the Whitehead Institute CGT.

Technology Updates

Labeling Kits

Affymetrix is retiring their old 3' Array kits in September 2009. In response, BMC has been evaluating new technologies. The newer kits are faster and require less starting material. We have selected the NuGEN technology as the primary labeling method we will be using going forward for eukaryotic arrays becuase of their ease and the modularity of their system that allows us to combine the processing of Affymetrix 3', Affymetrix Exon, and Agilent arrays. Information on the evaluation can be found HERE.. We DO NOT RECOMMEND mixing labeling types withing an experiment as we observed large differences between the absolute intensitites of signals between labeling methods. Arrays can still be hybridized using the Affymetrix 3'IVT, Affymetrix Exon and old Affymetrix 3' array by request (please ask for pricing).

We have also switched our prokaryotic labeling system from the Affymetrix system to one developed by Ambion. The Ambion sytem requires significantly less input RNA and has a more streamlined protocol. The Affymetrix labeling system is still available by request.

Small Cell Numbers

NuGEN has recently developed kits that allow the analysis of very small amounts of pruified RNA (100pg) or even single cells. Please contact Stuart Levine if you are interested in trying out these technologies.

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 provided 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.

Agilent Data Analysis

Agilent Scanner is available to members of the MIT Community without charge. 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.


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.

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