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2015 Sequencing Information

The leaves are changing and the weather is cooling, which can only mean: time to sequence some phage genomes!

A quick reminder 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.

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 20, 2015.

Quarter Schools

Please send your genomic DNA so that it arrives in Pittsburgh by Friday, January 8, 2015.

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. 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).

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 on "wet ice" (cold packs) with overnight shipping for delivery to Pittsburgh on Tuesday-Friday.

Address

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

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