Data Downloads

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.

How do we track file versions? (And what do the terms original, corrected, formatted, and standardized mean?)

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:

  • The first two numbers (x & y) indicate the version number of the contributed files submitted to the database by the contact/contributor:
    • "x" denotes major revisions, e.g. reflecting different quality levels)
    • "y" denotes minor revisions, e.g. reflecting minor adjustments to headers, minor error corrections, etc.
  • The third number (z) indicates the format-standardized versions of the contributed files, generated by the database team. These standard-format code-readable files are an essential step of loading the data into the graph database, and are also useful to project team members who code (and e.g. want metadata in a standardized format for import into R).
    There are three main steps to this format-standardization. These steps are given specific names, defined below, which are used in the download links to indicate the degree and type of processing applied to the contributed (i.e. original) file:
    1. corrected (if applicable): Corrections to the data itself, based on careful communication with the original data generator(s), but actually edited and saved by the database team.
    2. formatted: Formatting changes to simplify the original (or corrected) files. These include things like removal of merged cells and conversion of color-coded shading to text columns.
    3. standardized: Formatted text files with additional columns added (ending in __), which contain metadata in the database's standardized naming convention for Sites, Habitats, etc.

How do we track data quality?

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:

  • Quality 0: Unprocessed, raw data.
  • Quality 1: An internally-consistent dataset with basic processing, such as calibrations, background corrections, and quality control.
  • Quality 2: An externally-consistent dataset that is highly curated, in addition to undergoing the processing necessary for Quality 1. This should include all datasets that are part of peer-reviewed publications. DOIs are assigned to datasets in the Quality 2 category. The public side of the database will house mostly Quality Level 2 data.

Coring Sheets Terrestrial Subsurface Geochemistry Terrestrial Gas Fluxes Microbial Sequencing Viral Sequencing Plant Data Lake Data Remote Sensing Modeling

Coring Sheets

Palsa Core Pic
Photo credit: Virginia Rich
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)

Terrestrial Subsurface Geochemistry

Photo credit: Claire Wilson
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)

Terrestrial Gas Fluxes

Photo credit: Patrick Crill
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)

Microbial Sequencing

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)

Viral Sequencing

Photo credit: Pagaling and Haigh et al, 2007
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:
  • PowerSoil Bog: Replicate A (R1, R2)
  • PowerSoil Bog: Replicate B (R1, R2)
  • PowerSoil Fen: Replicate A (R1, R2)
  • PowerSoil Fen: Replicate B (R1, R2)
  • PowerSoil Fen: Replicate C (R1, R2)
  • Wizard Fen: Replicate A (R1, R2)
  • CsCl: Replicate A
  • CsCl Bead-beating: Replicate 1, 2, 3
  • CsCl Heat-treated: Replicate 1, 3
  • No CsCl Bead-beating: Replicate 1, 2, 3
  • No CsCl Heat-treated: Replicate 1, 2, 3
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: Accel-NGS 1S Plus library:

Plant-Associated Data

Photo credit: Nicole Raab
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)

Lake Data

Photo credit: Ruth Varner
Dataset Name (and download) Publication Contributor/Contact Readme Other Availability
Lake sediment microbiota.

Raw 16S rRNA sequencing reads: Metagenomic sequencing reads: Assemblies: 		Emerson et al. (2021) Nat. Commun. Joanne Emerson README
Lake water temperatures, 5- to 60-minute resolution.

All data (.zip file): Individual files: 		Wik et al (2013) J. Geophys. Res. Biogeosci., Wik et al (2014) Geophys. Res. Lett., Jansen et al (2019) J. Geophys. Res. Biogeosci., Jansen et al (2020) Geophys. Res. Lett. Patrick Crill README, sensor location map Bolin Centre

Remote Sensing Data

Photo credit: Nicole Raab
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

Modeling

Diagram credit: Virginia Rich
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.