Moore EisenNotes Eisen Notes iseem2

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Eisen lab Notes

Metagenomic sample gathering

Places to look for metagenomic samples

  • Short Read Archive
    • 134 marine samples. Appears to include GOS data. Has meta data associated with samples.
  • Camera (Split into projects instead of samples).
    • GOS
    • Antarctica Aquatic Microbial Metagenome
    • Mediterranean Bathypelagic Habitat Metagenome
    • Jack Gilbert's project (8 samples)
  • JGI
    • Nothing seems to be available but lots of projects are "available" for browsing under the "marine" filter for metagenomics projects.
  • MG-Rast
    • GOS - 88 samples - 12,358Mbp
    • HOT/ALOHA - 14 samples - 128Mbp
    • Chula Vista, CA Solar Saltern Study - 24 samples - 216Mbp
    • Jack Gilbert's samples - all 16S -
    • Surface Water Marine Microbial Community Gene Expression - Ian Hewson - 12 samples - 238Mbp
    • CaporasoIlluminaPNAS2011_3prime - 16S - 200+ samples


LOTS of overlap between the various portals.
Do we include all marine metagenomic samples ? Only water samples ? Viral metagenomic libraries ? Hydrothermal vents ? Marine Bacterioplankton ?


Guillaume Jospin downloaded samples from Camera in March 2013. They are available here All the following samples were submitted by Mary Ann Moran.

  • CAM_PROJ_CAM_P0000101 - Southeast US coastal marine system - Sapelo Island, GA - Filter min 0.2 - Filter max 3
    • PACT1 - Marsh Landing dock Control Sample 1
    • PACT2 - Marsh Landing dock Control Sample 2
    • PAPUT1 - Marsh Landing dock Treatment Sample PUT1
    • PAPUT2 - Marsh Landing dock Treatment Sample PUT2
    • PASPD1 - Marsh Landing dock Treatment Sample SPD1
    • PASPD2 - Marsh Landing dock Treatment Sample SPD2
  • CAM_PROJ_DayNight - Metatranscriptomic analyses of microbial assemblages (< 5 mm) from surface water at the Hawaiian Ocean Time-Series - Coordinates available.
    • DAYNIGHT_SMPL_METATRANSCRIPTOMIC_DAY
    • DAYNIGHT_SMPL_METATRANSCRIPTOMIC_NIGHT
  • CAM_PROJ_Sapelo2008 - Sapelo Island Summer 2008 Bacterioplankton Metatranscriptome - Coordinated available.
    • FN56
    • FN57
  • CAM_PROJ_DICE - Dauphin Island Cubitainer Experiment (DICE) - Coordinates available.
    • DICE_experimental
    • DICE_control
    • DICE_C1 - Dauphin Island
    • DICE_C2 - Dauphin Island
    • DICE_E1 - Dauphin Island
    • DICE_E2 - Dauphin Island
  • CAM_PROJ_PacificOcean - Influence of nitrogen-fixation on microbial community gene expression in the oligotrophic Southwest Pacific Ocean
    • 28 samples from different locations (coordinates available).
  • CAM_PROJ_SargassoSea - Sargasso Sea Bacterioplankton Community - Coordinates available
    • Sargasso Sea - Control
    • Sargasso Sea - DMSP
  • CAM_P_0000917 - Sapelo Island Microbial Observatory (SIMO) - Marine habitat, Georgia
    • 4 samples (descriptions/names are not informative)
  • CAM_PROJ_SapeloIsland - Sapelo Island Bacterioplankton Metagenome - Pyrosequencing
    • 8 samples (descriptions/names are not informative) all from the same location.