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Genotyping Technologies

Affymetrix GeneChips

Applied Biosystems Real Time PCR

Illumina BeadChips

Affymetrix Mapping Array Protocol

Mapping arrays are designed to provide genotyping information on the organism of choice. This data can be used for linkage analysis, haplotype mapping, association, and copy number variation. Affymetrix offers multiple levels of SNP densities to suit the needs of each investigator.

To view products, SNPs and mapping densities of available Affymetrix arrays, click here.

DNA Extraction

DNA extraction is performed by the investigators lab.The Required amount of DNA is 1μg. If you do not have this amount, then contact the Genomics Core for alternative options.

DNA Submission

To provide accurate results the initial DNA needs to meet basic quality control standards for concentration and purity. Samples not meeting these criteria cannot be guaranteed to produce viable data. Investigators will be notified if any problems prior to beginning any experiments. Samples must be of high quality 260/280 (ratio of 1.7-2.1). Integrity should be examined by gel electrophoresis.

Mapping chips in stock

Reaction Scheme

  • In separate reactions DNA is restriction digested with Nsp I and Sty I.
  • Complementary adaptors for each enzyme are added to digested DNA and ligated.
  • Multiple PCR reactions are performed to amplify the ligated DNA fragments.
  • PCR products are pooled and purified.
  • Purified products are then fragmented and end labeled with Biotin.
  • Biotinylated DNA fragments are then added to the chip and hybridized overnight.
  • The chip is then washed, stained and scanned.
  • Preliminary data analysis consisting of QC metrics will be run by the Genomics Core.

Affy Map

Viewing Your Data

Analyzed data will be provided in .txt, .csv, or .xls format available for download directly from our LIMS site. The raw data files will be available along with the analyzed data files.

Analysis of Your Data

A basic, preliminary data analysis will be performed by the Genomics Core staff. A dedicated data analysis computer is is located in the Genomics Core Building B room B111. Data analysis programs are available on this computer. To reserve this computer, sign up must be done through the Scripps Florida calendar system. If you require more in depth analysis of your data please contact Brandon Young.

Experiment Cost

To discuss actual prices for particular experiments, contact Brandon Young. Experiments will be processed with basic data analysis within 2 weeks of receipt of samples and sample submission form. You will be notified via e-mail if this is not sufficient time to complete the experiment.

Applied Biosystems PCR Protocol

Genetic mapping is designed to provide genotyping information on the organism of choice. This data can be used for linkage analysis, haplotype mapping, association, and copy number variation. Applied Biosystems offers single SNP density. PCR is a very useful as a means to validate SNPs identified by Affymetrix or Illumina mapping arrays. All assays are provided in single tube master mix format include labeled primers and Taq.

The equipment for this technology is provided by the Genomics Core in room 113C. The investigator is responsible for ordering all reagents and performing all experiments. The Genomics Core will help with experimental design as well as provide technical advice upon request.

An online calendar is used to sign up for time on the RT PCR machine. Be sure to use only the time you are signed up for. If you are going to use more time than you signed up for it is your responsibility to contact the next user and make sure it is acceptable to them. If you do not contact them, they have the right to stop your experiment before completion. If continued problems arise from any user the Genomics Core reserves the right to refuse use to that user.

To reserve time on the instrument, sign up using the Scripps Florida calendar system.

Prior to use of this equipment you must be properly trained by the Genomics Core.

To set up a training time, e-mail Brandon Young.

To view the validated SNP genotyping assays availble from ABI refer to their website.

RNA Yield

Reaction Scheme

  • DNA is added to reaction with SNP specific reporter labeled primers.
  • Multiple detection molecules are master mix Allele A -Vic, Allele B - FAM.
  • PCR Reactions are amplified in a standard thermocycler.
  • Reaction is read as an end point reaction upon completion of PCR steps.
  • Fluorescence signal is detected by reading on ABI 7900HT.
  • Detection VIC and FAM determines genotype AA, AB, or BB.
  • ABI software performs all calculations.

Taqman Method

Viewing Your Data

Data files are saved on a network shared drive in a folder provided for each individual (Gentech_RTPCR_name). This shared drive can be mapped to any computer at Scripps Florida. If you need help mapping a drive contact the IT department at flhelpdesk@scripps.edu

Analysis of Your Data

Analysis is performed by the user with free ABI SDS software. The software is available on a disc kept in the Genomics core. If you require more in depth analysis of your data please contact Brandon Young

Experiment Cost

Pricing is determined based on average usage per year per lab. In order to use the ABI Real Time System, a lab must purchase time on the machine. For specifics on the cost structure, see our Pricing List.

Illumina Mapping Array Protocol

Mapping arrays are designed to provide genotyping information on the organism of choice. This data can be used for linkage analysis, haplotype mapping, association, and copy number variation. The Genomics Core offers multiple levels of SNP densities to suit the needs of each investigator.

Illumina genotyping chips come in multiple densities. The high density chip (500K-1M SNPs) is run as one reaction, with the medium density (500-2000 SNPs) run in a 96-well format.

To view products, SNPs and mapping densities of available Affymetrix arrays, click here.

DNA Extraction

DNA extraction and purification is performed by the investigators lab. The required amount of DNA is 250ng. If you do not have this amount, then contact the Genomics Core for alternative options.

DNA Submission

To provide accurate results the initial DNA needs to meet basic quality control standards for concentration and purity. Samples not meeting these criteria cannot be guaranteed to produce viable data. Investigators will be notified if any problems prior to beginning any experiments. Samples must be of high quality 260/280 (ratio of 1.7-2.1). Integrity should be examined by gel electrophoresis.

Mapping chips in stock

  • Mouse Medium and Low Density Arrays
  • Human 500K SNP Array
  • Human 1M SNP Array
  • All other chips will require additional time for ordering.

Reaction Scheme

  • DNA is activated for binding to paramagnetic particles.
  • Activated DNA is combined with oligos and paramagnetic beads.
  • Extend, ligate and cleanup SNP specific oligos.
  • Amplify the SNP specific oligos with universal dye-labeled PCR primers.
  • Purify labeled DNA and hybridize to array overnight.
  • Wash and stain and scan SAM or beadchip.
  • Preliminary data analysis consisting of QC metrics will be run by the Genomics Core.

Viewing Your Data

Analyzed data will be provided in .txt, .csv, or .xls format available for download directly from our LIMS site. The raw data files will be available along with the analyzed data files.

Analysis of your Data

A basic, preliminary data analysis will be performed by the Genomics Core staff. A dedicated data analysis computer is is located in the Genomics Core Building B room B111. Data analysis programs are available on this computer. To reserve this computer, sign up must be done through the Scripps Florida calendar system. If you require more in depth analysis of your data please contact Brandon Young.

Experiment Cost

See Pricing List for general guidelines. To discuss actual prices for particular experiments, contact Brandon Young. Experiments will be processed with basic data analysis within 2 weeks of receipt of samples and sample submission form. You will be notified via e-mail if this is not sufficient time to complete the experiment.