1. What are the facility's hours of operation?
2. Where is the facility located?
3. When can I expect to get my results back?
4. What do I need to provide for a microarray?
5. What do I need to provide to have nucleic acids analyzed by the Agilent 2100 Bioanalyzer?
6. In what form are the results?
7. What are the costs of the services?
8. How do I pay for use of the facility?
9. Who is eligible to use the facility?
10. Do you have a list of the genes available for the human and mouse arrays?
11. How do I set up a new user account for using Vector NTI?
12. How do I access Vector NTI from a different computer?
13. I can't get a license when I try to access Vector NTI. What do I do now?

1. What are the facility's hours of operation?

The facility is open Monday through Friday during regular business hours.

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2. Where is the facility located?

The facility is located in room 6064 of the Rosenstiel Medical Sciences Building. Driving directions are available on the Contact Page.

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3. When can I expect to get my results back?

Microarray results will be delivered in a week, although many times the results come back sooner. Agilent results usually come back by the end of the next day.

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4. What do I need to provide for a microarray?

You can provide tissue, cells, or RNA. A little background on our procedures may be helpful here. A microarray experiment starts with the Trizol extraction of total RNA from tissue or cell culture. Total RNA is qualified on the Agilent Bioanalyzer to asses whether or not the RNA is intact. If the yield of total RNA from the Trizol extraction is too little (< 15 micrograms), we must amplify the RNA by using the Ambion Amino Allyl MessageAmp II aRNA Amplification kit. If the RNA is of high quality, we use it as a template in a reverse transcription reaction to produce Cy3 or Cy5 labeled cDNA. These probes are then hybridized to an oligo microarray. Because of the many steps involved in the protocol, this provides several possible entry points for the user to provide sample. It's up to the user to provide one of the following (for each sample) for us to process:

[** NOTE: In each case, the amounts are the minimum.]
Tissue: 100 milligrams (frozen)
Cell Culture: 5 million cells (washed with PBS, pelleted, on ice, or in the flask)
Total RNA: 20 micrograms (in nuclease-free water, on ice)

Smaller amounts may be allowed if agreed by the facility.
Please have each tube labeled clearly and unambiguously.

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5. What do I need to provide to have nucleic acids analyzed by the Agilent 2100 Bioanalyzer ?

Each sample that you wish to have analyzed on the Agilent should be provided to the facility in TE (Tris-EDTA) solution at a concentration of at least 50 nanograms per microliter. The concentration should not exceed 250 nanograms per microliter. It is permissible to use nuclease-free water in place of TE. Please deliver your samples on ice and have each tube labeled clearly and unambiguously. The Agilent can run 12 samples at a time. It is a good idea to also label the tubes 1 through 12 to define the exact lanes you wish each sample to be in.

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6. In what form are the results?

The results of an Agilent run are printed out and show the electropherograms and the simulated gel-like results for each of the samples. The data allows the user to assess the quality of the samples. A representative of our facility will gladly assist the user in the interpretation of the results. As an option, we can create a PDF file of the results and email them to the user.

The microarray results are distributed in CD-ROM format with a user friendly interface that is viewable in most internet browsers. Upon scanning of the post-hybridized array, a graphical file in TIFF format is produced. This file is then analyzed with software to compare the Cy3 and Cy5 channels for each of the features on the array. Raw and normalized numbers are generated for each of the features for each of the channels. This large amount of data is included in both a text file and in Excel format. Along with all the graphic files and data files that are generated, we also include a quality control reports for each microarray. To assist in the user’s mining of the data for significant results, we include an Excel file that lists differentially expressed genes along with the genes’ hyperlinks to NCBI and Genecard. We are also in the process of finding the best way to provide ontological data to the user so that the user may have a better understanding of the array results. Since the array process utilizes the Agilent BioAnalyzer to analyze the quality of RNA, BioAnalyzer results are also provided.

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7. What are the costs of the services?

The cost for each service can be found on the Microarray Facility's Services Pricing Page.

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8. How do I pay for use of the facility?

Payment for services is through an IDR (Interdepartmental Requisition Form). Please fill out an IDR and use account number 101766 as the Credit Account Number. Please deliver the IDR to Lubov Nathanson on the Medical Campus using locator code R-189 and RMSB as the building and 6064 for the room number. Instructions are available for filling out the IDR Form.

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9. Who is eligible to use the facility?

The facility is for the research community at the University of Miami. Anyone wishing to use the facility outside of the University of Miami should speak to the facility director Richard Bookman.

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10. Do you have a list of genes that are available for the human and mouse arrays?

A list of available arrays with links to their gene lists can be found on the Arrays Services page.

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