A list of datafiles from the IsoGenie project that can be downloaded directly, organized thematically. If you use this data in your research, please cite the accompanying manuscript(s) and contact the contributing PI.
Each dataset may have multiple versions and/or quality levels available. The most easily accessible files listed on this page should be the latest versions, but older versions (if applicable) can also be downloaded under "Old version(s)".
Expand the panels below for detailed descriptions of our version and quality level systems.
Data versioning is distinct from quality levels; it refers to the version of a dataset. As the data files are updated and published on the IsoGenieDB Data Downloads page, the database team (Ben Bolduc & Suzanne Hodgkins) assigns version numbers as "x.y.z" (0.0.0, 1.0.1, 2.0.0, etc.), starting from 0.0.0, with the following numbering convention:
In addition to versions, the data should also be assigned quality levels. As this requires intimate knowledge of the dataset and its respective discipline, we request that project members specify each data file’s quality level during submission to the IsoGenieDB.
In a nutshell, the quality numbers indicate the level of confidence that the data reflects "reality". Note that unlike version numbers, the quality level of a given dataset may be changed retroactively. For example, a Quality 1 dataset may be downgraded to Quality 0 if errors are discovered late in the processing pipeline, or upgraded to Quality 2 after passing peer-review. The basic definitions of the three quality levels are as follows:
Sampling Date(s) | Contributor/Contact | Files (from least to most processed) | Readme | Quality | Current version & date | Old version(s) |
---|---|---|---|---|---|---|
Coring Sheets for 2010-2011 | Virginia Rich | original, formatted (xlsx, csv), standardized | 1.5 | 0.0.5 (2021-11-15) | ||
Coring Sheets for 2012 | Virginia Rich | original, formatted (xlsx, csv), standardized | 1.5 | 0.0.4 (2021-11-15) | ||
Coring Sheets for 2013 | Virginia Rich | original, formatted (xlsx, csv), standardized | 1.5 | 0.0.4 (2021-11-15) | ||
Coring Sheets for 2014 | Virginia Rich | original, formatted (xlsx, csv), standardized | 1.5 | 0.0.4 (2021-11-15) | ||
Coring Sheets for 2015 | Virginia Rich , Sky Dominguez , Suzanne Hodgkins | corrected original, formatted (xlsx, csv), standardized | general field notes, handwritten field sheets | 1.5 | 1.0.2 (2021-11-15) | |
Coring Sheets for 2016 | Virginia Rich | original, formatted (xlsx, csv), standardized | 1.5 | 0.0.4 (2021-11-15) | ||
Coring Sheets for 2017 | Virginia Rich | original, formatted (xlsx, csv), standardized | general field notes | 1.5 | 0.0.3 (2021-11-15) | |
Coring Sheets for 2018 | Virginia Rich | original, formatted (xlsx, csv), standardized | 1 | 0.1.2 (2022-07-18) | ||
Coring Sheets for 2019 | Virginia Rich | original, formatted (xlsx, csv), standardized | 1 | 0.1.0 (2021-11-15) |
|
|
Coring Sheets for 2020 | Virginia Rich | original, formatted (csv), standardized | 1 | 0.0.0 (2021-11-15) | ||
Coring Sheets for 2021 | Virginia Rich | original, formatted (csv), standardized | 1 | 0.0.1 (2022-07-18) |
|
Dataset Name | Publication/Citation | Contact | Main data files (from least to most processed) | Standard error files (from least to most processed) | README | Current version & date | Old version(s) |
---|---|---|---|---|---|---|---|
Peat geochemistry 2010-2012 | Hodgkins (2016), Ph.D Thesis, Florida State University | Suzanne Hodgkins , Jeffrey Chanton | original, formatted, standardized | original, formatted, standardized | variable descriptions: original, standardized | 1.0.2 (2020-06-12) | |
Pore gas geochemistry 2010-2012 | Hodgkins (2016), Ph.D Thesis, Florida State University | Suzanne Hodgkins , Jeffrey Chanton | original, formatted, standardized | original, formatted, standardized | variable descriptions: original, standardized | 1.0.2 (2020-06-12) | |
Pore water geochemistry 2010-2012 | Hodgkins (2016), Ph.D Thesis, Florida State University | Suzanne Hodgkins , Jeffrey Chanton | original, formatted, standardized | original, formatted, standardized | variable descriptions: original, standardized | 1.0.3 (2021-11-15) | |
Incubation CH4 and CO2 production and δ13C for peat collected in July 2014 | Wilson et al. (2019) Front. Earth Sci. | Rachel Wilson , Jeffrey Chanton | corrected & formatted (with standardized columns) | README | 0.0.2 (2020-09-23) | ||
Methane oxidation data from Malhotra and Roulet (2015) transects, including incubation-derived oxidation rates, and in situ pH, Eh, and concentrations of dissolved CH4 and electron acceptors (O2, SO4, NO3, Mn, & Fe) | Perryman et al. (2020) | Clarice Perryman , Ruth Varner | main incubations and porewater, additional experiments 1 and 2 | variable descriptions & citation | 0.0.0 (2020-03-13) | ||
210Pb, 14C, and bulk density for cores and porewater collected in 2011-2014 and 2016 | Holmes et al. (2022) Global Biogeochem. Cycles | Beth Holmes , Jeffrey Chanton , Carrie McCalley (contact for 2016 field notes) | original | field notes and core map for 2016 cores (not from autochamber sites, but similarly named) | 1.0.0 (2022-01-16) | ||
Area-normalized FT-IR absorbances for the peat and plant species across the three main habitat types (palsa, bog, fen) | Wilson et al. (2022) STOTEN | Rachel Wilson | original | file descriptions (for all files associated with this manuscript) | 0.0.0 (2022-01-26) | ||
Log-transformed FT-ICR MS peak intensities for the dissolved organic matter and the extracts of solid peat across the three main habitat types (palsa, bog, fen) | Wilson et al. (2022) STOTEN | Rachel Wilson | original | file descriptions (for all files associated with this manuscript) | 0.0.0 (2022-01-26) | ||
Dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) in the porewater from the fen (E) and bog (S) sites | Wilson et al. (2022) STOTEN | Rachel Wilson | original | file descriptions (for all files associated with this manuscript) | 0.0.0 (2022-01-26) |
Dataset Name (and download) | Publication/Citation | Contributor/Contact | README | Current version & date | Old version(s) |
---|---|---|---|---|---|
Autochamber Fluxes 2002-2007 |
Bäckstrand et al (2010). Biogeosciences. Jackowicz-Korczyński et al (2010). J. Geophys. Res. Holst et al (2010). Atmos.Chem. Phys. Bäckstrand et al (2008). Tellus. Bäckstrand et al (2008). J. Geophys. Res. |
Patrick Crill | README | 0.1.0 (2018-08-04) | 0.0.0 |
Daily CH4 and CO2 fluxes (from LGR at autochamber sites) and peat temperatures (from InterAct Fen tower), 2012-2018 | Holmes et al. (2022) Global Biogeochem. Cycles, Varner et al. (2022). InterAct Fen peat temperatures originally from Swedish Infrastructure for Ecosystems Sciences (SITES) data portal. |
Beth Holmes , Patrick Crill | 0.0.0 (2022-01-05) | ||
Thaw pond bubble fluxes (2012-2015) and temperatures (2013-2018) | Burke et al. (2019) J. Geophys. Res.: Biogeosci. | Sophia Burke , Ruth Varner | fluxes README, temperatures README | 0.0.0 (2019-05-31) |
Dataset Name & Link | Publication | Contact | Detailed Links / Downloads | Current version & date | Old version(s) |
---|---|---|---|---|---|
Microbial and viral sequencing metadata | See publications listed in file. | Ben Bolduc | 0.0.0 (2019-12-16) | ||
Mapping of sequencing sample names to standardized sample metadata from the DB | Suzanne Hodgkins , Virginia Rich | 0.1.0 (2021-11-04) | |||
Candidatus 'Methanoflorens stordalenmirensis' draft genome (built from bog metagenomes in BioProject PRJNA215012) | Mondav & Woodcroft et al. (2014) Nat. Commun. | Gene Tyson | draft genome, source bog metagenome | 0.0.0 | |
iTags (2010-2011) (BioProject PRJNA215012) | Mondav & Woodcroft et al. (2014) Nat. Commun., Mondav et al. (2017) Environ. Microbiol. |
Gene Tyson | pyrosequencing runs
1,
2,
3,
4,
5; sample metadata (from Mondav et al. 2017 Table S1) |
0.0.0 | |
iTags (2011) (BioProject PRJNA235935) | McCalley et al. (2014) Nature, Deng et al. 2017, Mondav et al. (2017) Environ. Microbiol. |
Gene Tyson |
pyrosequencing run 6, sample metadata (from Mondav et al. 2017 Table S1) |
0.0.0 | |
Metagenomes, metagenome-assembled genomes (MAGs), and metatranscriptomes (2010-2012) (BioProject PRJNA386568) | Woodcroft & Singleton et al. (2018) Nature, Singleton et al. (2018) ISME J., Martinez et al. (2019) Syst. Appl. Microbiol. |
Gene Tyson | metagenomes, MAGs, metatranscriptomes | 0.0.0 | |
Caldiserica/Cryosericum MAGs and associated iTags (BioProject PRJNA482249) | Martinez et al. (2019) Syst. Appl. Microbiol. | Virginia Rich | MAGs, iTags | 0.0.0 | |
Fen metaproteomes (2010) (PXD000410) | Mondav & Woodcroft et al. (2014) Nat. Commun. | Virginia Rich |
data
(TR1,
TR2,
TR3), additional info (TR1, TR2, TR3) |
0.0.0 | |
Metaproteomes (2012) (PXD009096) | Woodcroft & Singleton et al. (2018) Nature, Martinez et al. (2019) Syst. Appl. Microbiol. |
Virginia Rich | 0.0.0 | ||
Comparison of microbial communities (and associated data) from anaerobic incubations and field samples | Wilson et al. (2021) PLOS ONE, Wilson et al. (2019) Front. Earth Sci. (iTag data) | Rachel Wilson , Ben Woodcroft , Ahmed Zayed |
|
0.0.0 (2021-02-03) |
Dataset Name | Publication | Contributor/Contact | Data Link(s) |
---|---|---|---|
Quantitatively-amplified dsDNA viromes, collected 2014 | Trubl et al. (2016) PeerJ, Trubl et al. (2018) mSystems | Gareth Trubl , Virginia Rich , Matthew Sullivan | raw reads |
Viral population contigs (1907 total), based on:
|
Emerson et al. (2018) Nat. Microbiol. | Joanne Emerson , Matthew Sullivan | viral contigs |
Trubl Soil Viromes | Trubl et al. (2019) PeerJ | Gareth Trubl , Virginia Rich , Matthew Sullivan |
QC reads:
|
Quantitatively-amplified ssDNA and dsDNA viromes, Nextera XT and Accel-NGS 1S Plus libraries, collected 2016-2017 | Roux et al. (2019) PeerJ | Gareth Trubl , Virginia Rich , Matthew Sullivan |
Metadata:
Roux et al. (2019), Table S1 (includes links to detailed QC reads with JGI login) Nextera XT library:
|
Dataset Name | Publication | Contact | Data Links(s) | README | Current version & date | Old version(s) |
---|---|---|---|---|---|---|
iTag-based microbial abundances from the rhizosphere and phyllosphere, and comparison with bulk peat (2016) | Hough et al. (2020) Front. Microbiol. | Moira Hough | Processed data:
OTU table,
mapping file,
network topology Raw data files: sequence file, barcodes, mapping file |
0.0.0 | ||
Log-transformed FT-ICR MS peak intensities for plant samples across the three main habitat types (palsa, bog, fen) | Wilson et al. (2022) STOTEN | Rachel Wilson | original | file descriptions (for all files associated with this manuscript) | 0.0.0 (2022-01-26) | |
Biomass coverage of plant species across the three main habitat types (palsa, bog, fen) | Wilson et al. (2022) STOTEN | Moira Hough , Rachel Wilson | original | file descriptions (for all files associated with this manuscript) | 0.0.0 (2022-01-26) |
Dataset Name and Link(s) | Readme | Publication | Contact |
---|---|---|---|
Stordalen Mire ground cover classifications, based on 2014 WorldView 2 satellite imagery | related GIS files (xml, ovr) | Varner et al. (2022) | Michael Palace |
For the Stordalen Mire ground cover classifications, probability of the neural network assigning each cover class (see publication for details): H2O, HM, OT, RK, SW, TG, TS, WT | Varner et al. (2022) | Michael Palace | |
Drone imagery (2014) over Stordalen Mire | Palace et al. (2018), Varner et al. (2022) | Michael Palace |
Name | Input & Output Files | Model Code | Readme | Contact | Publication/Citation |
---|---|---|---|---|---|
Ecosys model products for Stordalen, 1901-2010 | reconstructed climate forcing inputs, model output | executable program, source code | model inputs description | Kuang-Yu Chang , William Riley | Chang et al. 2019, The Cryosphere. |
Ecosys model products for Stordalen, 2011 | reconstructed climate forcing inputs, model output | executable program, source code | model inputs description | Kuang-Yu Chang , William Riley | Chang et al. 2019, JGR Biogeosciences. |