BioMicroCenter:Microarrays

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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

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.

SAMPLE TYPES

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

Eukaryote	Min.RNA	Min.Vol.	Platforms	Notes
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
CGH	3ug	6 μL	Agilent	labeling using Agilent's CGH kit
small RNA	1ug	6 μL	Agilent	labeling using Agilent's miRNA arrays

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 or Agilent 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. Currently the average turn around time is currently 2-3 weeks.

ARRAY SELECTION

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.

Agilent vs. Affymetrix

AFFYMETRIX arrays are very high density arrays of 30mer oligonucleotides built by lithography. An Affymetrix probeset is composed of numerous neighboring perfect match and mismatch probes that are combined and used in the calculation of intensity and relative expression. Affymetrix arrays are the most common arrays used in genomics right now and have a rich bioinformatic architecture that allows for a large number of analyses. While expression arrays are the most common, Affymetrix also creates arrays for SNP calling and ChIP-chip. Affymetrix expression arrays come in two flavors: 3' and exon. 3' arrays use oligo dT priming while exon arrays amplify from the whole RNA using random primers. Affymetrix arrays are one-color arrays and use biotinylated nucleotides in the cRNA/cDNA to recruit HRP-peroxidase to the probes. Affymetrix arrays come as single arrays from a broad list of species. The BioMicro Center has a hybridization oven, two 450 fluidics devices and a 7G scanner for handling Affymetrix arrays.

AGILENT arrays are lower density arrays then Affymetrix, but have much longer oligos (60mers) and are printed on glass slides using dot-matrix printing technologies. Because this method does not require the creation of metal plates, novel microarray designs cost no more then designs created by Agilent. Agilent arrays can be used for a variety of assays including gene expression, ChIP-chip, miRNA hybridization, and CGH. Our Agilent scanner can handle Agilent arrays of up to 250k probes per slide (Donated by the Bell lab). Because of the lower probe density and the longer oligos used, each probe is evaluated separately. Each glass slide can contain multiple identical arrays (2, 4, or 8), reducing the cost per hybridization, often below the level of Affymetrix arrays. Typical mammalian expression arrays are in a 4x44k format where each slide contains four identical arrays that are seperable by a gasket slide. Agilent arrays can be hybridized either as one-color or two-color using Cy5 and Cy3 labeled cRNA/cDNA. 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.

Labeling Methods

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 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.

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 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.

LINKS

Obtaining your results

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. Information on downloading your data is in the link above.