Genomics and Proteomics Core Laboratories

MyGPCL Login | Register

Register Directory Protocols Forms Pricing

Research Services - DNA Specimen Processing

DNA Specimen Processing Overview

	The Genomics and Proteomics Core Laboratories are able to provide DNA extraction services for a broad range of application needs. We are available to perform DNA extractions from whole or frozen blood, tissue, cultured cells, buccal cells, and cell lines for downstream processes including sequencing, SNP detection, genotyping, positional cloning and MicroArray printing.

About the Facility

	The GPCL Specimen Processing Core Laboratory is located on the 3rd floor of 3343 Forbes Ave. The purpose of the facility is to extract and purify high quality DNA and RNA, and to perform Cell Culture. Call (412) 648-9528 to contact the laboratory supervisor. The mailing address is: University of Pittsburgh Genomics and Proteomics Core Laboratories 3343 Forbes Ave 3rd Floor Pittsburgh, PA 15213 There is a pre-PCR "clean room." Quality assurance checks are performed daily on all freezers, refrigerators, and cell culture incubators to ensure that proper conditions are maintained at all times. Routine inspections are performed to ensure that pipettors are calibrated every 6 months and that all hoods are annually certified. The laboratory is equipped with state of the art equipment. Major equipment housed in the laboratory includes: a dual chamber CO₂ incubator, laminar flow cell culture hood, vacuum pump, Hydra-96 robotic pipettor, refrigerated high speed centrifuge and microfuge, microscope, chemical fume hood, cryostorage tanks with level monitors, milligram balance, homogenizer, polytron, multiple water baths, refrigerator, -20°C and -80°C freezers.

Policies

	Confidentiality GPCL staff will maintain strict confidentiality of research projects for the investigators using the facility. The Specimen Processing Core Laboratory recognizes the importance of patient confidentiality, and ensures that confidentiality is maintained in line with IRB regulations and requirements and HIPAA guidelines. Facility Acknowledgement The Specimen Processing Core Lab requests an acknowledgement in the Methods section of any publications resulting from this data. An example is "DNA extraction was performed by the Specimen Processing Core Facility of the Genomics and Proteomics Core Laboratories at the University of Pittsburgh." We request that a copy of scientific papers and reprints be forwarded to the Core Director for all publications that come from our work. . Support Letter The Scientific Director will gladly provide investigators with a letter of support stating our willingness to assist you with your research. Please contact the Core Administrator for more information. Billing Billing is done on a monthly basis. For internal users, billing will be done automatically by interdepartmental charges (IDC). Users outside the university will receive an invoice by mail. Approval IRB approval must be obtained prior to sample intake and specimen processing for any research project involving human subjects. A copy of the IRB approval letter must be forwarded to the GPCL Administrator. Once all committee approvals are met, each project must be discussed with the core laboratory supervisor and facility director to determine sample receipt schedule and details of the study. See Scheduling/Shipping section for details.

DNA Specimen Processing Frequently Asked Questions

	Q: What type of DNA extraction method is employed? A: See DNA Extraction Method. Q: How should blood samples be collected and handled prior to shipping? A: See Blood Collection Guidelines. Q: How should the Specimen Tubes be labeled? A: See Blood Tube Lables. Q: What is the GPCL Laboratory schedule with respect to sample receipt? A: See Scheduling and Shipping. Q: Which type of blood tube should I collect my sample in? A: See Blood Collection. Q: What is the expected DNA yield from whole blood? from cultured cells? from buccal cells? A: Whole Blood: 16-50 ug/mL blood. Cultured Cells: 5-10 ug/1-2 Million cells. Buccal Cells: 0.2-4 ug/cytology brush. Q: What solution are DNA samples stored in? A: See Sample Storage.

Protocols and Procedures

	The GPCL Specimen Processing Core Laboratory uses standard operating procedures and optimized conditions. In order to see that all samples are processed in a timely fashion, and to maximize the probability of high quality DNA we suggest that the following guidelines be followed. Blood Collection For DNA extraction, collect blood in EDTA (purple-top) tubes. Vacutainer Blood Tubes from Becton Dickinson are recommended. For serum, collect blood in Serum Separator Tubes, SST (red-gray top) tubes. Vacutainer Blood Tubes from Becton Dickinson are recommended. Blood Tube Labels All sample tubes must be labeled with the following information in order to be processed: the Study Name, PI Name, Study Reference ID, and the Date Collected. Any other pertinent information regarding the sample must be noted, i.e. infectious status (if known). A computerized spreadsheet indicating this information must be enclosed with each shipment. See notification section in Scheduling/Shipping for further details. Tissue / Cell Collection Please contact the Specimen Processing Supervisor for information regarding tissue and cell collection guidelines and extraction methods. IRB Considerations Any human sample collected must be done so following all relevant IRB restrictions and HIPAA regulations. DNA Extraction Method DNA is extracted from samples according to the manufacturer's instructions using the Gentra Puregene DNA Isolation Kit. The extraction is based on a modified salt precipitation method. Quantitation / Qualitation Once DNA is isolated, the DNA quantity and quality is checked using a spectrophotometer. The concentration and purity is measured by reading the Absorbance at 260 nm and 280 nm wavelengths. The expected range of high quality DNA preparations based on the A260/A280 nm wavelength ratio should be 1.7-2.0. Should the ratio deviate from this range, it may indicate protein or RNA contamination, and the sample would require repurification. Sample Storage Following extraction the DNA is stored at 4°C in DNA Hydration Solution, which is supplied with the Gentra Puregene DNA Isolation Kit. Reporting The Investigator is provided with a printout and/or computer copy of the Absorbance at 260 nm and 280 nm wavelengths, A260/A280 nm wavelength ratio, the DNA concentration and the total yield of DNA.

Scheduling and Shipping

	In order to ensure timely processing of your samples and the quality of the DNA that we are able to extract, please conform to these basic shipping and scheduling guidelines. Contact us Before any samples may be shipped, the study and investigator must be registered with GPCL. If you have not yet contacted us, you may contact us by phone, email or register as a user at our web site registration page. Packaging All specimens must be packaged and mailed in containers that conform to postal regulations. Notification A sample log sheet must be received with all samples. A standard sample log sheet can be emailed to the investigator to be used for all sample drop-offs. Shipping Ship samples Monday through Wednesday using Next Day Delivery. Samples are received Tuesday through Thursday to ensure receipt and to allow for tracking and shipping errors. If other shipping dates are required, arrangements must be made with the Specimen Processing supervisor. Blood collected in EDTA (purple-top) Vacutainer tubes should be received for processing within 24 hours from the time of blood draw. Cells from cell culture may be shipped overnight with sufficient dry ice for subsequent DNA extraction. Drop-off Samples may also be dropped off at one of our sample dropoff locations. The dropoff locations are 3343 Forbes Ave Room 303, and S534A Scaife Hall. Please make prior arrangements by contacting the laboratory (See Personnel Directory) to assure that we know your samples have arrived. (412) 648-9528 University of Pittsburgh Genomics and Proteomics Core Laboratories 3rd Floor 3343 Forbes Ave Pittsburgh, PA 15213

Pricing

	Please see our pricing page.