biogem

Frequently Asked Questions

What is BIOGEM?

BIOGEM is the UCSD BioMedical Genomics Microarray (BIOGEM) Facility, and was established in February 2000 at UCSD to meet the needs of scientists interested in microarray technology. Scientific questions pertaining to BIOGEM should be directed to Dr. Gary Hardiman. Billing and pricing questions pertaining to BIOGEM should be directed to Cyndy Illeman, Core Resources, UCSD Health Sciences.

What are the facility's hours of operation?

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

What are DNA microarrays?

Microarray technology, primarily advanced by Pat Brown and colleagues at Stanford University, makes use of a robotic spotting device or "microarrayer" to spot DNA sequences onto glass slides. These arrays are then hybridized with fluorescent cDNA or cRNA probes. More information is available on our publications page.

Where is BIOGEM located at UCSD?

BIOGEM is presently located in The Leichtag Family Foundation Biomedical Research Building. Directions are available.

Our ship-to Address is

Attention James Sprague
BIOGEM
(BioMedical Genomics Microarray Facility)
University of California San Diego
Room 172
The Leichtag Family Foundation Biomedical Research Building
9500 Gilman Drive
La Jolla CA 92093-0724

How do I contact BIOGEM ?

E-mail is the preferred method for contacting Dr. Gary Hardiman <ghardiman@ucsd.edu> and Cyndy Illeman <cilleman@ucsd.edu>.

What general services do you offer?

Agilent RNA Bioanalyzer Service
Processing of ABI, Codelink, Illumina, and Agilent array platforms
Custom DNA array fabrication
Array hybridization
Scanning and image analysis
Data archiving
Training and consulting

How much do your services cost?

Please see our Pricing Page.

What array processing services does BIOGEM offer?

BIOGEM currently offers processing of commercial array platforms including ABI, Agilent, Illumina, and Codelink platforms.

Which platform should I use?

For more information on the various microarrays platforms available at BIOGEM, please read the following review articles.

Microarrays - Comparisons and Contrasts. Pharmacogenomics 5(5), 487-502.
Biochip platforms as a functional genomics tool for drug discovery. Current Opinion in Drug Discovery & Development: 8(3) 347 (2005).

Do you have a list of genes that are available for Agilent oligonucleotide arrays and Amersham codelink bioarrays?

Yes. For links to company pages containing gene lists, please see the Gene List pages for the Codelink, and Agilent array platforms. For ABI array content, please visit the Applied Biosystems website.

How should I prepare and provide RNA to BIOGEM?

The most critical aspect of any microarray experiment is the quality of the RNA. RNA should be prepared in accordance with the platform being utilized. For detailed instructions on RNA preparation and submission see the following pages:

How do I go about submitting RNA samples for microarray analyses?

Please make sure you have read the information on RNA extraction on the RNA submission page and have filled out the appropriate online submission page. Failure to provide complete information will delay the processing of your chips. Co-ordinate with James Sprague to drop off your samples. She can be reached by telephone at (858) 822-4231 or email at james@microarrays.ucsd.edu.

When can I expect to get my results back?

Microarray results will typically be delivered within two to three weeks. Work in the facility is performed on a "first come, first served" basis. The turnaround time is dependent on the number of customer samples undergoing analysis at the time and the availability of the particular chips.

How do I retrieve the data?

After you are assigned a username and password you may download your data from BIOGEM's website. Your data can also be made available via an ftp site on the BIOGEM server.

What information and data will I actually receive?

The scanned chip images are provided as ".tif" files. The raw data is provided in an Excel spreadsheet that has been crunched and extracted from the image data. It has been subjected to a preliminary analysis with the fold change listed of differentially expressed genes. Pathway and ontology analyses are also provided as part of the service.

What costs are typically associated with a microarray experiment?

The costs of a microarray experiment include the cost of the chip itself, the reagents for labeling the RNA target, and a labor component. Please see the Pricing page for more details.

How should the RNA be sent and addressed?

The RNA should be sent overnight on dry ice to the ship-to address listed above. All RNAs will be stored in -70°C freezer at the facility.

My RNA is precious. Will any of my left over material be returned to me?

The amount of RNA required for an experiment ranges from 50ng - 5ug total RNA. Please provide as much as possible, 2 - 5ug if available. We keep the residual in case the labeling fails the first time. We return any RNA we do not use if requested. Customers' RNA will be stored for three months following the experiment, after which it will be discarded.

I do not want to run an array experiment but have RNA samples that I would like analyzed on an Agilent Bioanalyzer (nanochip or picochip assay).

BIOGEM provides a service whereby we run customer RNA samples on the Agilent Bioanalyzer to determine whether the integrity of the RNA sample(s) in question is good. Priority is given to users for whom we are running microarray experiments at a cost of $10 per sample. For customers not requesting microarray experiments, there may be a waiting period. During times of high volume activity, the turnaround time time may be one to two weeks. There is a minimum charge of $100 to run up to 10 samples. Additional samples can be run at a cost of $10 per sample. Please see the Agilent Bioanalyzer page for more details.

What clone collections are available at BIOGEM ?

BIOGEM has the sequence-verified mouse and human unigene cDNA collections, which were acquired from Incyte/Genome Systems. The Drosophila EST set cDNA (DGC1) collection was obtained from the Berkeley Drosophila Genome Project (BDGP). See the Clone Collection page for more details on which clones are available. Due to the complexity of the licensing arrangements with the vendors, we are unable to provide the complete sets to other researchers. However individual clones or groups of clones are available to UCSD investigators. Please note, owing to licensing issues, these clones are only available to UCSD researchers. Please contact James Sprague for more details.

Do you fabricate and process home-made or boutique microarrays?

Since its inception BIOGEM has fabricated a mouse 10k array, a Drosophila 5k array, a human 10K array and a Yeast Genome Array. In 2004 these arrays were retired. Please contact Dr. Gary Hardiman if you require information on these arrays.

Does BIOGEM fabricate custom arrays?

BIOGEM does not offer custom printing to non-UCSD Investigators. Microarrays can be printed by UCSD Investigators from clone sets or oligonucleotides. Typically the researcher will carry out the up-front work in DNA preparation or oligonucleotide design. For further information and pricing please contact James Sprague.

Can BIOGEM prepare DNA probes for the fabrication of custom arrays?

BIOGEM can carry out the up-front work in DNA preparation and purification and print customized DNA arrays. Contact Dr. Gary Hardiman for pricing and details.

Does BIOGEM process Affymetrix Gene Chips ?

No, BIOGEM solely provides alternative microarray services to Affymetrix chips. Access to the Affymetrix GeneChip. System is available through the Gene Chip Core Facility (http://www.vmrf.org/research-websites/gcf/index.html).

Does BIOGEM have an Affymetrix Gene Chip Scanner?

No, BIOGEM currently does not have a scanner that is compatible with Affymetrix Gene Chips.

Does BIOGEM provide quantitative real-time PCR (qRT-PCR) services?

No, currently BIOGEM does not provide quantitative real-time PCR services. For quantitative real-time PCR, investigators should contact the CFAR genomics core.

Does BIOGEM offer help with data analysis?

BIOGEM will provide assistance to UCSD investigators with data analysis only for data generated in the facility. The rate is $100 per hour. Contact Dr. Gary Hardiman for details. Priority is given to UCSD investigators who are doing experiments with BIOGEM.

I am not a UCSD researcher, but work at a non-profit organization. Can I purchase arrays and have access to facility services?

Yes, BIOGEM can provide the products and services described above. There is an additional charge of 45% on top of the fees described above. Contact Cyndy Illeman for details.

I am a researcher in a biotech/pharmaceutical company. Can I purchase arrays and have access to facility services?

Yes, BIOGEM can provide the products and services described above. There is an additional charge of 100% on top of the fees described above. Contact Cyndy Illeman for details.

As a UCSD customer, how do I pay BIOGEM?

Payment for services for UCSD investigators is through a UCSD departmental IFIS index.

As an outside non-UCSD customer, how do I pay BIOGEM?

Prior to sending samples to BIOGEM, non-UC clients should provide Cyndi Illeman with a formal company Purchase Order including all terms with current billing address and this should be signed by official company purchasing agent. Payment should be made payable to UC REGENTS and ONLY after the UCSD Invoice is received by your accounting office. Payment should include remittance advice copy per invoice instructions. DO NOT SEND PAYMENT WITH PO. Final rate to be billed is at the determination of BIOGEM.

I have a UCSD affiliation (as I am an Adjunct Professor or Visiting Scientist at UCSD). I work at another institution. Do I pay the UCSD rate?

Payment at the UCSD rate is only possible if done using an IFIS index. If payment is made using a Purchase Order, then there will be an additional charge of 45% on top of the fees described above

Last Updated March 2008
By Dr. Gary Hardiman