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FROGER - Functional Re-annotation of Oyster Genomes with Epigenetic Resources

Funded by USDA NRSP-8 Aquaculture small project grant

Date: May 21 - 23 (half day)

Goals

  1. Annotating Epigenetic features in the Eastern Oyster Genome (EOG)

    • DNA methylation
    • Chromatin associated proteins
    • Transposable Elements
    • miRNA
    • lncRNA
  2. Comparison of DNA methylation quantification methods in the EOG

    • WGBS - Whole Genome Bisulfite Sequencing
    • MBD-BS - Methyl Binding Domain enrichment followed by bisulfite sequencing
    • MSPI - Reduced representation digestions with MSPI

Projected Products

  1. Annotation for EOG and gap analysis for improved epigenetics annotation approaches

  2. Manuscript on methods comparison for DNA methylation data - target: Frontiers in Marine Science Special Issue: Marine Environmental Epigenetics

Participants

  • Hollie Putnam - URI
  • Steven Roberts - UW
  • Jose Eirin-Lopez - FIU
  • Kevin Johnson - LSU
  • Sam Gurr - URI
  • Jon Puritz - URI
  • Katie Lotterhos - NEU
  • Alan Downey Wall - NEU
  • Bodie Weedop - NEU
  • Yaamini Venkataraman - UW
  • Mackenzie Gavery - NOAA
  • Shelly Trigg - UW

Data Sources

Detailed Schedule

May 20th Arrive PVD in the afternoon and be transported to Hampton Inn

  • Dinner as at group meet in Lobby at 5:45pm
May 21st 08:00 meet in parking lot for transport to URI Alton Jones Campus Whispering Pines
  • Breakfast at the hotel

09:30 - Introductions, Annotation Data resources
11:00 coffee break
11:15 - 12:30 - Data Overview and Gap analysis
12:30 Lunch
1:30 - 3:15 - Annotation work
3:15 Coffee Break
3:30 - 5:00 Annotation work and summary of day
5:00 - 5:30 Introduction to data for day 2 methods comparison
6:00 dinner

May 22nd

08:30 - Overview for day 2 methods comparison
09:30 - 11:00 - Data Analysis and methods writing
11:00 coffee break
11:15 - 12:30 - Data Analysis and methods writing 12:30 Lunch
1:30 - 3:15 - Annotation work
3:15 Coffee Break
3:30 - 4:30 Data Analysis and methods writing
4:30 - 5:30 Summary of progress for day 2, Setting goals and timelines for two products
6:00 dinner

May 23rd

08:30 - Overview for sections and timeline
09:30 - 11:00 - Breakout Groups
11:00 coffee break
11:15 - 12:30 - Breakout Groups and summary 12:30 Lunch

Departure or continue on to Genomics workshop

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