SEA-PHAGES Logo

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

2022 MRA Workflow

2022 MRA Workflow
 

Purpose
The MRA workflow is designed to support you (SEA faculty) and your students publish MRAs describing phages that you and your students discover and characterize as part of the PHAGES project. Participation is this workflow is only a requirement for those who are offered a discounted publication fee, though we welcome any and all faculty to participate and/or use workflow resources. As always, we’re happy to work with you individually if you have any questions or concerns, so please do not hesitate to reach out. Please direct any MRA Workflow-related questions to Vic Sivanathan.

The workflow includes the following 4 components, which you should click to read more about:

  1. Timeline
  2. Writing Guidance
  3. Internal Review
  4. Publication Fees

1. Timeline:

This timeline was developed to enable the program to support as many faculty publish MRAs on an annual basis. This year, SEA faculty have identified ~ 100 genomes to be included in this workflow. We are grateful to our SEA Faculty on the SMART Team who will aim to get these genomes  QC’ed and in GenBank by the end of June. It is therefore critical that your annotations be submitted on time, by May 1. Those annotations submitted after May 1 may be delayed in their submission to GenBank.

  • Feb 15, 2022: Sign-up by this date to participate in this MRA workflow.
  • May 1, 2022:  Submit your annotated genome for QC by this date. Genomes will be QC’ed and submitted to GenBank by June 30, 2022.
  • July 15, 2022: Complete a Review-to-Improve analyses of the pre- and post-QC'ed annotations, then submit your manuscript for internal review by this date.
  • Oct 31, 2022: By this date, finalize your MRA manuscript based on feedback from internal review. Note that you can submit your manuscript for publication as soon as internal-review feedback has been incorporated.

Note: If your annotated genomes do not require QC, that is if you are an Expedited Submitter or a SMART member, or if you are writing an MRA for genomes already in GenBank, your abbreviated workflow is as follows:

  • Feb 15, 2022: Sign-up by this date to participate in this MRA workflow.
  • May 1, 2022: Submit your annotated genome and MRA manuscript to SEA for submission to GenBank and review, respectively, by this date.
  • Oct 31, 2022: By this date, finalize your MRA manuscript based on feedback from internal review. Note that you can submit your manuscript for publication as soon as internal-review feedback has been incorporated.

2. Guidance for Writing your MRA:

  1. Please use the SEA Faculty Resource on QUBES for “Writing Microbial Resource Annoucements (MRA)”.
    This resource includes 3 primary components:
    • A template MRA that describes the information required for each section of the MRA, how to locate this information, as well as sample text and links to sample publications.
    • A data collection sheet, which we recommend you and your students  use to gather and house all the information you will need for the MRA. You will need to submit this data sheet (or the same compilation of data for your phage in another format) along with your manuscript to facilitate internal review.
    • A faculty checklist, which you can use to make sure you have included in your manuscript all the requested information. You will also need to submit this checklist along with your manuscript for internal review.
      Note: The resource was recently updated (Feb 2022), so please download the most recent version.
  2. If you intend to publish on multiple phages, you can do so by writing a single manuscript describing multiple phages or writing multiple manuscripts. Phages need not be closely related (e.g. same cluster or same host) to be included in one publication. Suggestions for formatting the information for multiple phages are provided in the MRA Template. Please note, however, that this year each school is only eligible to be considered for one MRA at the discounted price of $150.
  3. We recommend you begin the process of writing your manuscript early in the semester. For example, the initial part of your manuscript will describe characteristics of the phage(s) that were uncovered as part of the Phage Discovery component of the course, and this information can be gathered and entered into the Data Collection Sheet even before you begin annotating the genome.

3. Internal Review
This year, the SEA Team will perform the internal review. Next year, we hope to formalize the review process and invite SEA faculty to participate as reviewers.

4. Publication Fee

The current regular publication fee is $800 for ASM members and $1,100 for non-members. This year, ASM will charge a discounted publication fee of $150 for a limited number of submissions from the SEA. Priority for the discounted rate will be based on the following criteria:

  • First, for faculty who do not have access to funds to cover publications fees and have not previously published an MRA.
  • Second, for faculty who do not have access to funds to cover publications fees but have previously published an MRA.
  • Third, for faculty who have access to funds to cover publications fees but have not previously published an MRA.
  • Fourth, for faculty who have access to funds to cover publications fees and have previously published an MRA.

The SEA Team will notify those selected and not selected for this discounted rate for 2022 by email.

 

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 17 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.

Current Events

Phage Discovery Workshop 15A

June 25, 2022 to July 1, 2022

Upcoming Events

Phage Discovery Workshop 15B

July 9, 2022 to July 15, 2022

Recent Events

2022 SEA Symposium

April 8, 2022 to April 10, 2022

Forum Activity

cdshaffer posted in Frameshift in BM cluster phages?

Debbie Jacobs-Sera posted in Genome Curation - a must read!

Kathleen Cornely posted in Frameshift in BM cluster phages?

FORUMS HOME PAGE