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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.