Moore Notes 7 3 13

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Group Call

  • Participants: Josh, Guillaume, Ladan, Katie, Jonathan
  • Josh: Shotgun metagenomics sequencing
    • Existing samples
      • Discussed sequencing some of the EMP samples with Rob Knight
      • Jack Gilbert and others could potentially fill gaps in ecological, geographic distribution
      • Need hundreds of samples for global modeling
    • Citizen science beach samples
      • Separate effort
      • Need to think about how to collect, etc.
      • May be hard to get environmental data at needed resolution due to heterogeneity along coast line
      • How quickly does it need to be frozen? Depends on the volume of material needed, could use buffers instead if not much needed
      • Josh: To sample coastal air, could sample with clean petri dishes (no media)
    • How many sequences per sample minimum?
      • Rob Knight: 1 million (based on standard in literature)
      • Tom: Power to see differences will depend on abundance of protein family, may want 5 million to see rarer protein families
    • Multiplexing
      • Can do 32 samples/lane
      • This gives 6 million reads per sample
    • Costs (with Tom)
      • Library prep per lane (without multiplexing) = $140-200
      • Sequencing per lane of Hi-Seq = $1400-2000
      • Total for 200 samples with multiplexing?
    • Jonathan will get quote from BGI facility at UC Davis
  • Guillaume: integrating MRC and PhyloSift
    • Schedule call with Aaron for afternoon or during his August visit
    • Jonathan: talked with Aaron, who wants to be involved and thinks there will be challenges
  • Hiring
    • Sarah Hird will work on biogeography, starting next week
    • Gene family informatics is a priority
    • Functional diversity, metabolism prediction, biochemical diversity also a priority (Patrick Bradley?)