UGC Sample Submission Guidelines

To submit a research project request, please submit an online Project Inquiry and a Sample Submission Form. Samples will only be accepted after both forms have been completed.

For clinical samples, please just use the Clinical Requisition Form.

Feel free to contact us via email Genome_Center@upmc.edu, via phone 412-623-7155, or meet us in person (please email or call to schedule an appointment).

We provide service for:

  • Whole Genome Sequencing (WGS)
  • Whole Exome Sequencing (WES)
  • Whole Transcriptome Sequencing (total RNA-Seq)
  • mRNA sequencing (mRNA-Seq)

Submission Instructions

1.  Sample Type

We accept premade libraries, purified DNA/RNA for library preparation, or fresh frozen tissues/cells, blood or saliva for DNA/RNA extraction. Once sequencing is complete, we can provide bioinformatics analysis as requested. 

A.  Whole Blood

A minimum of 3 mL whole blood in EDTA or ACD tubes (heparin is not desired, please confer with the laboratory prior to submission), ship with cold not frozen gel-pack to minimize heat damage DO NOT FREEZE. Specimens older than 72 hours are not acceptable for molecular analysis.

B. Saliva

Saliva or buccal wash with preservative shipped at ambient temperature with cold not frozen gel-pack if temperature along transit route is anticipated to be above 75oF.

C. FFPE

Slides or FFPE blocks shipped with frozen gel-pack if temperature along transit route is anticipated to be above 75oF.

D. Cell pellets

Cell pellets purified by Ficoll gradient or differential lysis are preferred. They may be suspended in PBS or RPMI and shipped with cold not frozen gel-pack if temperature along transit route is anticipated to be above 75oF. Frozen cell pellets either dry or in freezing media ship frozen on dry ice. Please note the type of media on the requisition.

E. Purified DNA/RNA Samples for Library Preparation Requirement

Please submit samples in tubes provided from us (you can pick them up when you’re ready to submit) as they are used with our laboratory robotics to process the samples. Or use 1.5 ml Lo-bind microfuge tubes. Each tube must be clearly labeled numerically (1, 2, 3, etc.) followed by the sample name (ie. 1-AB10001). Tubes should be submitted in order as listed on the submission form (left to right, up to bottom, not randomly placed, and not loose/unracked) on any type of box/rack designed to hold the tubes. Sample quantification is required prior to submission. Samples should be dissolved in EDTA-free solution such as nuclease-free water or 10 mM Tris-Cl (pH 8.5). Extracted RNA must be shipped frozen on dry ice.

NOTE: Concentrations determined by absorbance-based method such as NanoDrop are very unreliable. Please quantify the DNA and RNA concentrations using fluorescence-based method such as Qubit or PicoGreen. If you cannot do fluorometry, please send us 2X the minimum amount that NanoDrop determines. We typically request more sample amount than we need to allow for any repeats that we may need to perform. If your sample amount should be limited for any reason, you may submit a reduced sample volume. Please contact us for discussing available options.

Sequencing Type

Minimum
Quantity

Minimum
Volume

Quality

Minimum Concentration

WGS

2 µg

110 µL

 

>15 ng/µL

WES

2 µg

110 µL

 

>15 ng/µL

Total RNA-Seq

500 ng

50 µL

RIN>7

10 ng/µL

mRNA-Seq

1 µg

50 µL

RIN>8

20 ng/µL

 

F. Prepared Libraries Requirement

Please bring us undiluted libraries. We’ll do QC (Fragment Analyzer and qPCR) on all the libraries you brought, and dilute and denature them according to Illumina’s prototol. We do NOT guarantee cluster yield or quality for libraries prepared outside of UGC, but we are happy to answer any questions you have regarding library preparation.

NOTE: Before making your libraries, please make sure your barcodes are compatible with Illumina Standards.

 

  2.  Sample submission

Please send an email notification at least 48hr ahead of time for your sample arrival to make sure that your samples will be received and stored properly.

 

Schedule your drop-off

Please call 412-623-7155 or email us to schedule a time to drop off your samples. You can find our direction and parking information https://ipm.pitt.edu/UGC/contact-us.

 

Drop-off and shipping address

Please review the FedEx holiday schedule to make sure that your samples will be delivered without delay.

UPMC Genome Center

5560 Centre Ave

Pittsburgh, PA 15232

Drop-off hours: Monday–Friday, 9:00 AM – 4:30 PM

 

MedSpeed address

If you’re using MedSpeed Courier and just search Hoechstetter or our ID, it should pop up.

Hoechstetter Bldg-Genomics

5560 Centre Ave

Suite:2 FL

Pittsburgh, PA 15232

ID: 172530