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)

Location: URI Alton Jones Campus Whispering Pines

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

• Qiagen Data (method comparison)
• LSU Oil Exposure Data
• Resequencing Data

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