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.
BioMicro Center Services
>> THIS PAGE IS CURRENTLY BEING EDITED <<
We are currently set up to primarily handle expression analysis. Our service includes:
- 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.
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. Below are a list of different sample types and our recommended labeling methodologies:
The BioMicro Center has extensive experience handling samples for expression analysis.
|Prokaryote||1 μg||6 μL||Affy or Agilent||labeling using Ambion for Affy arrays|
|3' Array (std)||50ng / 100pg||6 μL||Affy or Agilent||labeling using NuGEN for Affy arrays.|
|Exon Array||50ng / 100pg||6 μL||Affymetrix||labeling using NuGEN for Affy arrays|
|small RNA||1ug||6 μL||Agilent||labeling using Agilent's miRNA arrays|
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.
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. Currently the average turn around time is currently 2-3 weeks.
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 allows us to 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.
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 because 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 within an experiment as we have observed large differences between the absolute intensities 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 system 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 purified 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 for $50 per scan. 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.
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 for you the download.
- There is a Windows applications client called SSH Secure Shell available at :
- Instructions to use the application can be found Instructions to use SSH .
- There is a Macintosh client called Fetch 5.3.for Macintosh.
- It can found http://ist.mit.edu/
- Select software : File transfer – Macintosh
- Direction for installing and using Fetch are located here:
Accessing the server.
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.