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The official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program.

The SEA-PHAGES Program

SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester, discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses, but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses.

The program aims to increase undergraduate interest and retention in the biological sciences through immediate immersion in authentic, valuable, yet accessible research. By finding and naming their own bacteriophages, students develop a sense of project ownership and have a ready-made personal research project at a fraction of the cost of traditional apprentice-based research programs. Some of the positive effects of the SEA-PHAGES program have been reported here.

SEA-PHAGES is jointly administered by Graham Hatfull's group at the University of Pittsburgh and the Howard Hughes Medical Institute's Science Education division.

SEA-PHAGES IN THE NEWS

Sequencing Status 2021-22

Below is a live spreadsheet showing the status of SEA-PHAGES sequencing samples for the 2021-22 academic year. Generally, samples are only listed after they're scheduled for a MiSeq run, so don't worry if the samples you sent haven't appeared yet.

CLICK HERE to open this in a new browser window.

 

Sequencing Information: 2021-22

It's getting towards that time of year again: time to send SEA-PHAGES DNA samples in to be sequenced at Pitt!

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. Our shipping situation is still not 100% normal, and we want to make sure 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://docs.google.com/forms/d/e/1FAIpQLSfdhZpw1LHL42zxAotEVqhmrr8RBN9-kuPL_42ioYmuBU-4-Q/viewform

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, if you have one.

Deadlines

Semester Schools

Please send your genomic DNA so that it arrives in Pittsburgh by Thursday, December 2.

Quarter Schools

Please send your genomic DNA so that it arrives in Pittsburgh by Friday, January 7.

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

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 24 to Nov 28, and again from Dec 22 to Jan 3. 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: Becky Garlena
University of Pittsburgh
Langley Garage 120F
Langley Hall
Fifth and Ruskin Avenues
Pittsburgh, PA 15260
(412) 624 6976

Sequencing 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. The charge is usually $250 per genome for sequencing. Contact Andy Baltzegar at dabaltze@ncsu.edu for pricing and details.

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.

Archiving Information 2021-22

The procedure for sending archiving samples to the University of Pittsburgh is largely similar this year, but please read carefully.

Note that you do not need to add beads to tubes anymore.

Contact Us/Questions

Please send any questions about the information below to Debbie (djs@pitt.edu) and Becky (rag4@pitt.edu).

Please read the latest Archiving Instructions at the link below.

https://phagesdb.org/protocols/96/

Archiving 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.

We are asking that you add a tracking number in the appropriate place on the form. We have rotating lab staff, and want to make sure all packages are accounted for.

https://forms.gle/EJHBmBsk1YRbo4gW6

Timeline

PLEASE ARCHIVE BY CALENDAR YEAR! That is, send all samples found in 2021 together, regardless of whether they were found in spring, summer, or fall.

You should send archiving samples for phages found in 2021 for arrival no later than December 16.

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 24 to Nov 28, and again from Dec 22 to Jan 3. Please avoid shipping during these times.

Please be sure to include an up-to-date Archiving Report in the package. You can print one from your institution's page on seaphages.org.

Shipping Address

Attn: Becky Garlena
University of Pittsburgh
Langley Garage 120F
Langley Hall
Fifth and Ruskin Avenues
Pittsburgh, PA 15260
(412) 624 6976

DNA Samples

Just a note that DNA 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.

Upcoming Events

Cohort 14 Phage Genomics Workshop (Dec 2021)

December 6, 2021 to December 17, 2021

Recent Events

Forum Activity

Debbie Jacobs-Sera posted in Tomas tRNA error

cdshaffer posted in Tomas tRNA error

Lee Hughes posted in Tomas tRNA error

FORUMS HOME PAGE