Working with the Microbial Sequencing Center at Pitt

Guidelines for Sequencing with Us

What is the best way to ship my samples?
In general, ambient temperature overnight shipping is adequate for DNA samples.  For samples that are on the lower end of the concentration range or being shipped during the warmer months of the year, shipping with ice packs or dry ice is recommended.  RNA samples must be shipped frozen on dry ice as they will degrade readily. Samples needing extraction should be sent on sealed petri dishes at room temperature, or as frozen pellets with ice packs or dry ice.

For all shipments, please ensure your samples are protected during transit by placing them in a secondary rigid container, if you are not using a box.

How should I extract my DNA/RNA?
Most column-based extraction kit will provide favorable results.  For internal samples, our lab has long used Qiagen Blood and Tissue kits.  Other methods of extraction will also work if care is taken to remove contaminants.  For RNA samples, we would recommend Qiagen RNeasy kits with DNase treatment.

What’s the best way to quantify my samples before sending them?
Qubit is the preferred method of quantification as it is far more accurate measuring double-stranded DNA only.  Nanodrop is also acceptable, though we ask that you aim for 10x the required concentration. 

How much coverage do I need for my samples?
There is no one answer to this question as it depends on how you intend to use your data.  For an application such as reference-based variant calling, we recommend at least 40x average coverage of your genome.

How long until I receive my data?
Starting from the day that we receive your DNA/RNA samples, you will receive your sequencing data within 14 days.  The wait is often less than this and it is not uncommon to receive data the same week that the samples were provided.

How will I receive my data?
Your data will be uploaded to your own personal folder on Box and a link will be shared with all email addresses listed on your intake form.  The data will be available to you for 1 year and additional users can be added upon request.

There are 2 files in each folder, what are they?
The data contained within your folder will be comprised of .fastq files for 150bp paired end reads, labeled R1 and R2 for the forward and reverse reads.  These are raw, unassembled files that come directly from the sequencer (though the Illumina adapter sequences have been trimmed off during the demultiplexing process).

What forms of payment are accepted?
We accept purchase orders. Please submit POs through the contact form. For international customers, we also accept wire transfers.