The days are getting shorter, and the lysate titers are getting higher... It must be sequencing season!
Contact Us/Questions
Please send any questions about the information below to Dan (dar78@pitt.edu) and Becky (rag4@pitt.edu).
Sample Submission Form
Please submit the information about the samples you are sending using this Google Form. This will help us keep track of samples, correct any spelling errors, and make sure your samples are accounted for. Please fill out a copy of this form for each sample you are submitting. The best time to fill it out is as you are getting your shipment packed, so that when your box arrives, we'll already have the information on your phages in our database.
If possible, please add a tracking number in the appropriate place on the form to help ensure all packages are accounted for. Please note whether each sample is a "Priority" or "Backup" in the Notes field, along with any other info we should have.
https://forms.gle/9aHqQyB7mwZqZHyZ8
Quantity
Each SEA-PHAGES school may have two genomes sequenced per Bioinformatics section that it is teaching during the current academic year. Please indicate any order of preference for which samples to prioritize, if you have one.
Deadlines
Getting samples in early, if you have them ready, is always appreciated!
Semester Schools
Please send your genomic DNA so that it arrives in Pittsburgh by Tuesday, November 26, 2024.
Quarter Schools
Please send your genomic DNA so that it arrives in Pittsburgh by Wednesday, January 8, 2025.
If you will have trouble meeting these deadlines for any reason, please contact us.
Guidelines for DNA
Buffer
Samples that are resuspended in TE are problematic, since the EDTA may interfere with enzymatic shearing of the DNA. You can resuspend your DNA in Elution Buffer (Tris), T(1/10)E, or in purified water.
Amount
We need a minimum of 3 µg (micrograms) of genomic DNA. If you're in the ballpark of this number but not quite there, contact Dan and Becky to see if it's okay.
Concentration
At least 40 ng/µl. Ideal is 100-300 ng/µl. If you're above 300 ng/µl please consider diluting to a workable concentration and workable volume. Shipping a volume less than 20 µl is not recommended. Keep in mind that spec-based quantifications (like Nanodrop) count all absorbance at 260 nm, not just genomic DNA, so they often overestimate the real concentration. Please err on the high side of the amount of DNA you send when possible.
Gel Picture
Please submit—either via email or in the shipping box—an image of the gDNA being run on an agarose gel. We use these to look for sample integrity (not already sheared/degraded) and purity (no RNA).
Labeling
Please clearly label the tubes you are sending with the name of the phage as it appears on PhagesDB. Don't label tubes using student's initials only, or other ambiguous names like "Phage1" or "PittPhage". If possible, put a small circular sticker on the top of the tube and write the phage name only on it.
Shipping
Please ship samples, as described below, for delivery to Pittsburgh on Mon-Thurs. We sometimes have issues with Friday deliveries, and don't want any samples to sit over the weekend.
Also, we are unable to receive samples from Nov 27 to Dec 2, and again from Dec 23 to Jan 2. Please avoid shipping during these times.
Packaging
We prefer standard microcentrifuge tubes, and strongly recommend wrapping the caps with Parafilm to prevent spilling or evaporation. The tubes can be packed into a 50 ml conical tube with some KimWipes to stabilize them during shipment. If shipping overnight (preferred), you can actually just send the samples at room temperature, as the DNA should be fine for 24 hours in transit. If shipping on a slower schedule, you should use cold packs. Aim for delivery to Pittsburgh on Tuesday-Friday. If shipping near holidays, please check with us about when we'll be around to receive samples.
You can include a packing slip with any information you think we should have about the enclosed phages.
Address
Attn: Dan Russell
University of Pittsburgh
303 Clapp Hall
4249 Fifth Ave
Pittsburgh, PA 15260
(412) 624-6976
Sequencing Additional Samples
For the past decade, the Genomics Sciences Laboratory at NC State has provided high-quality, for-cost sequencing services to schools in the SEA-PHAGES program who wish to sequence additional genomes beyond those allotted by the program. The charge is usually $225 per genome for sequencing. Contact the NC State sequencing core at gslncsu@gmail.com for details. Make sure they're not using a tagmentation library prep!
Archiving Samples
Just a note that archiving samples should be sent to the same address as above, and so if it's convenient to you, you can send DNA samples and archiving samples together in a single box.