Public Metagenomes We Use
From EdwardsLab
Lab Usable Metagenomes
There are lots of metagenomes out there, and we also have some data for other people that we are processing but that has not been published. People still like to retain control of their data, and so it is our practice to not use data that has either (i) not been published, or (ii) we have explicit consent that we can use the data without requiring to include the originators in subsequent publications that may stem from our research. Its just easier that way.
Available metagenomes
This table contains a list of the metagenomes that we can use, and the metadata assoiated with them. Feel free to update this table as and when you get more metagenomes!
Note that you can get to the citations for these papers by taking the PMID number and searching for it at PubMed.
| Internal ID | Name | Usable | Library Type | Project | PMID | Source | Contact | Type | Other Key Words | Coordinates | Collection Date | Time | Depth | Temperature | Salinity | Height above floor | Volume (L) | Current (m/s) | Atmosphere | Chlorophyll (mg/L) | DOC (mg/L) | POC (mg/L) | phosphate | nitrite + nitrate? | Nitrite | Ammonium | TIN | PON | # microbes | # VLP |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 41 | Soudan Red Stuff | Yes | Microbial | Mines | 16549033 | Rohwer Lab | Rob Edwards | Mine | Terrestrial; Subterranean | 47.819307,-92.242595 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| 42 | Soudan Black Stuff | Yes | Microbial | Mines | 16549033 | Rohwer Lab | Rob Edwards | Mine | Terrestrial; Subterranean | 47.819307,-92.242595 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| 43 | Marine Phages GOM | Yes | Viral | Ocean Viruses | 17090214 | Rohwer Lab | Florent Angly | Marine | Bay; Seawater; Aquatic | 25.571,-92.883; 26.839,-94.999; 27.489,-96.273; 27.547,-96.473; 27.733,-96.841; 27.838,-97.052; 27.467,-97.417; 27.501,-88.402; 27.969,-87.58; 28.562,-87.414; 29.001,-87.297; 26.475,-85.641; 25.313,-84.72 | 06/01/94 - 07/31/01 | - | 0 - 164 | 14.7 - 30.5 | 26.1 - 40.6 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| 45 | Marine Phages BBC | Yes | Viral | Ocean Viruses | 17090214 | Rohwer Lab | Florent Angly | Marine | Gulf; Seawater; Aquatic | 49.849,-124.434; 50.186,-124.857; 50.197,-124.848; 50.028,-124.732; 50.079,-124.714; 49.975,-124.683; 50.005,-124.964; 50.122,-124.904; 49.727,-124.323; 49.828,-124.796; 50.190,-125.142; 48.801,-123.403; 49.558,-123.79; 49.682,-123.847; 49.774,-123.975; 49.731,-123.738; 49.607,-123.803; 50.295,-124.727; 50.116,-125.314; 49.950,-125.138; 49.950,-125.098; 49.455,-123.285; 49.574,-123.253; 49.661,-123.221; 50.059,-125.246; 50.023,-125.208; 50.114,-125.309; 49.978,-125.192; 49.972,-125.179; 48.586,-123.506; 48.604,-123.502; 48.669,-123.502; 50.162,-123.892; 49.733,-124.246; 49.130,-123.467; 49.300,-123.233; 49.328,-123.735; 48.817,-125.133 | 08/01/96 - 07/31/04 | - | 0 - 245 | 7.0 - 22.6 | 14.0 - 31.3 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| 46 | Marine Phages Arctic | Yes | Viral | Ocean Viruses | 17090214 | Rohwer Lab | Florent Angly | Marine | Seawater; Aquatic | 71.729,-155.157; 72.500,-160; 72.900,-158.8; 72.500,-157; 74.585,-158.492; 74.250,-162.56; 73.667,-164.113; 72.500,-151.333; 70.875,-133.967; 70.367,-133.6; 70.367,-133.6; 69.896,-139.5; 69.400,-138; 70.200,-137 | 09/01/02 - 10/31/02 | - | Feb-46 | -6.9 | 20.3 - 35.0 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| 53 | Marine Phage SAR | Yes | Viral | Ocean Viruses | 17090214 | Rohwer Lab | Florent Angly | Marine | Seawater; Aquatic | 32.167,-64.5 | 6/30/05 | - | 80 | 19.8 | 36.7 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| 63 | MAM.1 | Yes | Microbial | Marine | - | Moran Lab | Mary Ann Moran | Marine | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| 64 | MAM.2 | Yes | Microbial | Marine | - | Moran Lab | Mary Ann Moran | Marine | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| 65 | MAM.3 | Yes | Microbial | Marine | - | Moran Lab | Mary Ann Moran | Marine | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| 66 | MAM.4 | Yes | Microbial | Marine | - | Moran Lab | Mary Ann Moran | Marine | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| 72 | Porites coral samples | Yes | Microbial | Coral | 17922755 | Rohwer Lab | Linda Wegley | Coral | - | 9.351608, -82.256717 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| 137 | MAM.1.1 | Yes | Microbial | Marine | - | Moran Lab | Mary Ann Moran | Marine | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| 138 | MAM.2.1 | Yes | Microbial | Marine | - | Moran Lab | Mary Ann Moran | Marine | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| 139 | MAM.3.1 | Yes | Microbial | Marine | - | Moran Lab | Mary Ann Moran | Marine | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| 140 | MAM.4.1 | Yes | Microbial | Marine | - | Moran Lab | Mary Ann Moran | Marine | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| 164 | Lean Mice | Yes | Microbial | Obesity | 17183312 | Gordon Lab | Peter Turnbaugh | Animal Associated | Mice; Intestine; Lean Mice | 38.634620,-90.262847 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| 165 | Obese Mice | Yes | Microbial | Obesity | 17183312 | Gordon Lab | Peter Turnbaugh | Animal Associated | Mice; Intestine; Obese Mice | 38.634620,-90.262847 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Table source
The table is easier to maintain as a tab separated list so that you can edit it in open office or excel or whatever. The table can be accessed from the lab internal wiki if you have a password.
