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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. 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
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 room 113M bench 19. 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.
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.
Reaction Scheme
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. 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
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 room 113M bench 19. 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.
Sequenom Genetic Mapping Genotyping services using the Sequenom Mass Array system is recommended for searching or characterizing known SNPs. This platform allows for easily customizable assays. This system is ideal for fine mapping of regions identified from Affymetrix or Illumina arrays. DNAs should be submitted in 96-well format at a concentration of 10ng/μl, with a minimum of 20μl total volume. Actual parameters may differ slightly; hence a consultation is required at the beginning of the project. Contact Brandon Young.
Technology - iPLEX Assay The assay uses a beadless, label-free primer extension chemistry to generate allele-specific diagnostic products. Each of the primer products has a unique molecular weight that allows the associated genotype to be precisely identified using mass spectrometry. By measuring molecular weight directly, the system is capable of characterizing genotypes with unprecedented levels of accuracy.
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 room 113M bench 19. 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.
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