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2016 Sequencing Information

Sequencing time of year approaches once again!

Remember that each SEA-PHAGES school can have two genomes sequenced per in silico section they are teaching this year. We recommend that you send at least one backup sample in case one of your samples fails our QC. Please indicate any order of preference, if you have one.

Once again this year, all "official" (HHMI-supported) SEA-PHAGES sequencing will take place at the University of Pittsburgh. This post contains some basic info about prepping and shipping your DNA samples.

Deadlines

Semester Schools

Please send your genomic DNA so that it arrives in Pittsburgh by Friday, November 18, 2016.

Quarter Schools

Please send your genomic DNA so that it arrives in Pittsburgh by Friday, January 6, 2017.

If you will have trouble meeting these deadlines for any reason, please contact Dan Russell at dar78@pitt.edu.

Guidelines for DNA

Buffer

We can't use samples that are resuspended in TE. The EDTA interferes with enzymatic shearing of the DNA. You can resuspend your DNA in Elution Buffer (Tris) or in purified water.

Amount

We need a minimum of 5 µg (micrograms) of genomic DNA.

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. 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. Err on the high side of the amount of DNA you send.

Gel Picture

Please submit—either via email to dar78@pitt.edu 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

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. The shipment should be sent with cold packs and overnight shipping for delivery to Pittsburgh on Tuesday-Friday.

You can include a packing slip with any information you think we should have about the enclosed phages.

Address

Dan Russell
344 Crawford Hall
Department of Biological Sciences
4249 Fifth Avenue
Pittsburgh, PA 15260

Additional Samples

For the past several years, 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. Contact Andy Baltzegar at dabaltze@ncsu.edu for pricing and details.

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