Genotyping samples are fluorescently labeled PCR products generated by the user and run on our Applied Biosystems 3130XL or 3730XL instruments. Samples should be organized in 96-well PCR-type plates, or in 8-tube strip tubes. DO NOT use flat-bottomed plates as they are difficult to pipette from. We expect samples to be PCR products in buffer or water. We will also accept premixed products in formamide but you MUST inform us of this. We typically use 1 ul of a PCR reaction per run, adding it to 10 ul formamide mixed with the standard of choice. For multiplexed samples from multiple PCR reactions, more than 1 ul will likely be needed due to dilution, so let us know the specifics of these samples in an e-mail. Samples should be securely sealed with strip caps (recommmended) or plate sealing tape. For shipped samples it is especially important that the sealing method be secure against leakage, and samples packed to avoid crushing.

We support standard genotyping with Applied Biosystems dye sets D (4-dye set: 6FAM, HEX, NED, with ROX 500 as standard) and G5 (5 dye set: 6FAM, VIC, NED, PET, with LIZ 500 as standard), as well as SnapShot and SNPlex.

Please give samples reasonably short names, avoiding names longer than 23 characters or names with spaces, quotes, or slashes present. Organize samples in the plate to avoid gaps where possible. Samples MUST be organized in the 8-well dimension in plates, with samples running from 01A, 01B, 01C, etc.

Please use the following Excel spreadsheet (zipped for downloading) to place your order for standard genotyping and SnapShot: Genotyping_template.

Use the following spreadsheets (zipped for downloading) for SNPlex reactions, being sure to fill in the colored cells (96-well plates): SNPlex96_template.

or 384-well plates): SNPlex384_template.

Please e-mail the file to us at DNACore@DNAServer.bsd.uchicago.edu as an attachment, changing the name of the file to include your name and the date (eg. J-Doe_8-1-06.xls).

For analyzing your data, we have a copy of GeneMapper 4.0 on a user-accessible computer in the facility. Otherwise for simple sizing analyses, you can download a copy of Peak Scanner from the appliedbiosystems.com web site (Windows only). Third party software is also available (eg. Geospiza.com).