Clinical Genomics Facility FAQ
- Sample Submission EAQ
- Extraction Service FAQ
- miRNA Expression Service FAQ
- Expression Service FAQ
- Genotyping Service FAQ
- Results and Data Analysis FAQ
Sample Submission FAQ
How can I submit samples?
First you must fill out the Service Request Form. You must have a valid Pitt grant account number.
Upon receipt of the Sample Request Form, a service estimate will be drafted and emailed to the address provided in the contact field. Have your primary investigator review and sign the service estimate, then fax it back to our facility using the fax number on the estimate.
Once we have received both the Sample Request Form and a signed service estimate we can place your project in our queue and we will contact you to arrange drop-off of your samples.
What type of tubes should I submit samples in?
All tissue, cell pellets, DNA, and RNA should be submitted in 1.5mL or 2.0mL microcentrifuge tubes. Please bring your tubes over to the facility on dry ice in a freezer box, if possible.
How should I label my tubes?
Sample names must be clearly labeled on top of the tube and must exactly match names on the request form or they will be returned. Sample names cannot be longer than 12 characters in length.
Where do I drop my samples off?
Once a member of the CGF has contacted you to schedule sample drop off, you may bring your samples to the lab. We are located in Shadyside Hospital on the ground floor of the West Wing. When you arrive at Shadyside Hospital, follow the signs to the West Wing, then take the stairs to the ground floor (the elevators do not access our level). You will see the door for Pathology on your left – go through the door to the Pathology reception window, and please tell the receptionist that you are going to WG04.8 (Clinical Genomics Facility). Go through the reception office and follow the hall until it ends. Turn left, and the door will be on your right side; we share space with the TARPS facility (Tissue Bank). Ring the bell for admittance.
How much RNA/DNA is Required per Service/Assay?
| Service | Mass of RNA/DNA Required and Final Concentration | Volume of RNA/DNA Required |
|---|---|---|
| Nucleic Acid Quantification | ||
| QC with Bioanalyzer | N/A | 5 μl |
| OD Only | N/A | 5 μl |
| miRNA Expression Assays † | ||
| Agilent miRNA Platform | 100 ng Total RNA containing miRNAs | Up to 4 μl Total TNA containing miRNAs in nuclease free water (100 ng final conc.) |
| Exiqon miRNA Platform | 0.5-1 μg Total RNA containing miRNAs | Up to 2 μl Total RNA containing miRNAs in nuclease free water (0.5-1 μg final conc.) |
| Affymetrix Expression Assay | ||
| Affy RNA Expression Labeling and Whole Assay Services- One Cycle Kit | 1 μg Total RNA | Up to 8 μl Total RNA in nuclease free water (1.0 μg final conc.) |
| Affy RNA Expression Labeling and Whole Assay Services- Two Cycle Kit | 0.01-0.1 μg Total RNA | Up to 5 μl total RNA in nuclease free water (0.01-0.1 μg final conc.) |
| Ambion Expression Whole Assay- MessageAmp II-Biotin Enhanced kit | 0.05-1 μg total RNA | Up to 9 μl Total RNA in nuclease free water (0.05-1 μg final concentration) |
| Affymetrix Genotyping- Fresh Tissue | ||
| Affy DNA Genotyping- Xba 10K 2.0 Assay | 250 ng Whole Genomic DNA | Up to 5 μl Whole Genomic DNA in Reduced TE (250 ng final conc.) |
| Affy DNA Genotyping- 250K NSP/STY Assay | 250 ng Whole Genomic DNA | Up to 5 μl Whole Genomic DNA in Reduced TE (250 ng final conc.) |
| Affy DNA Genotyping- 5.0/6.0 Assay | 500 ng Whole Genomic DNA | Up to 10 μl Whole Genomic DNA in Reduced TE (500ng final conc.) |
| Affymetrix Genotyping- FFPET Samples | ||
| Affy DNA Genotyping- Xba 10K 2.0 Assay | 1.0 μg Whole Genomic DNA | Up to 5 μl Whole Genomic DNA in Reduced TE (1.0 μg final conc.) |
| Affymetrix Hybridization and Scan | ||
| Affy Hybridization and Scan | 15.0 μg fragmented cRNA | 30 μl fragmented cRNA (15.0 μg final conc.) |
| CodeLink Expression Assay - Please Inquire | ||
- These are the minimal amounts specified in the respective protocols. We recommend you provide us with excess in order to run QC analysis and to repeat assays if necessary.
- † Please Inquire if you wish to run a miRNA study within the CGF.
What happens to my samples once all requested services have been completed?
Once you receive your results, please contact Christin Sciulli or Maureen Lyons-Weiler (412-623-1497, cgf@upmc.edu) to schedule pickup of total RNA samples, DNA samples, biotin-labeled cRNA, and hybridization cocktails. The CGF will not store your samples long-term and will dispose of all unclaimed samples.
Whom do I contact with questions?
For questions concerning experimental design, grant proposals and budgets, technical issues, and availability of results, please contact Dr. William LaFramboise: laframboisewa@upmc.edu or 412-623-9746.
For questions concerning sample submission procedures, sample drop off, technical issues, and obtaining results, please contact Christin Sciulli or Maureen Lyons-Weiler: cgf@upmc.edu or 412-623-1497