Frequently Asked Questions (FAQ) |
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What does your lab charge per 96-well plate for genotyping? The center is designed as a low-cost genotyping facility
where researchers have complete control over their data. This is in
contrast to a core facility where you provide samples, and they are run
by others for you. By our design IGMC can provide genotyping services
for 1/3 the cost of a core facility. We have a nominal monthly fee. In addition, the basic genotyping cost for one gel that holds up to 96 samples is inexpensive and includes the use of a 377 sequencer for 4 hours, ingredients to make acrylamide gels and TBE buffer, formamide, data storage, and use of computers with data analysis software. The center sells supplies needed for running gels, such as membrane combs, filters, ROX size-standard, and pipette tips to name a few items. Customers are not obliged to purchase these items from the center. Contact the lab director for detailed information on current pricing. How will I learn to use the ABI 377 sequencers, access data, and analyze raw data files? Either the lab director or a highly experienced employee provides training in use of the ABI Prism 377 sequencers. In addition, the lab director provides instruction in the use of Genescan and Genotyper software. The lab director also sets up all server and computer accounts for customers and makes sure that folks can access data.
How do the ABI 377 sequencers work? Samples are run by electrophoresis on acrylamide gels and the labeled DNA fragments are separated by size. As the fragments pass through the “read region” a laser scans constantly across the gel exciting the fluorescent dyes attached to the fragments. The light intensities are then stored for a digital gel image and processing. The advantage of separating fluorescent fragments by acrylamide is the ability to multiplex many PCR products each lane, minimizing the cost per gel. How should I prepare my samples for genotyping on the ABI 377's? PCR products need a fluorescent label on the 5' end. Most users label with tags such as HEX(green), NED(yellow), and 6-FAM(blue). Other labels could include JOE(green), and 5-FAM(blue). ROX(red) is generally reserved for the standard in each lane. Universal M13 Primer option. In the first run-thru on the sequencer, do you help with optimization of PCR products? The lab manager can provide advice on optimizing, but the decision is ultimately up to the customer. Optimization is a trial and error process, but once samples are optimized, genotyping should proceed smoothly. Does IGMC provide a labeled ladder in each well for genotyping? We sell ROX size standards at cost. Size standards are typically used in each sample to ensure proper sizing of PCR products.
Accounts for the server are accessible from Windows, Macintosh, and Linux computers both inside and outside of the lab. Since all data at the laboratory are generated using Macintosh computers, use caution when copying or manipulating Macintosh files on other operating systems. What data transfer and storage options are available at IGMC? There are several options for moving and storing data when using our sequencers. Data can be stored on our server, a zip disk, or burned to a CD. All Macintosh computers associated with the sequencers are equipped with Zip drives (100 MB) for users to store and/or move data. Burning CDs is also a service the center can provide at a nominal charge.
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