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  1. Zenodo

    Title: GIANT: Galaxy-based Interactive tools for ANalysis of Transcriptomic data

    Software 2018

    Contributors:
    Summary:

    GIANT is a User-friendly tools suite for micro-arrays analyses and for exploring RNA-seq & Micro-Arrays differential results

  2. Zenodo

    Title: juliechevalier/GIANT: First Release of GIANT

    Software 2018

    Contributors:
    Subjects:
    • Transcriptomic
    • galaxy
    • micro-arrays
    • RNA-seq
    Summary:

    First Release of GIANT

    Galaxy-based Interactive tools for ANalysis of Transcriptomic data

    GIANT is a User-friendly tools suite for micro-arrays analyses and for exploring RNA-seq & Micro-Arrays differential results

  3. Zenodo

    Title: edgeR version 3.8

    Software 2014

    Contributors:
    Summary:

    edgeR is an R package distributed as part of the Bioconductor project (http://www.bioconductor.org). The Galaxy tool that implements this workflow is available from http://toolshed.g2.bx.psu.edu/view/shians/shrnaseq.

  4. Woods Hole Open Access Server

    Title: Microbial taxa (amplicon sequence variant or ASV) statistical analyses for two seagrass genotypes from wasting disease mesocosm experiments at Bodega Marine Laboratory in July-Sept of 2015

    Dataset 2022-11-22

    Contributors:
    Subjects:
    • climate change
    • host-parasite
    • microbiome
    • seagrass
    • wasting disease
    Summary: This dataset includes outputs from statistical analyses of differences in microbial taxa (amplicon sequence variant or ASV) abundance among two groups of seagrass, Zostera marina, genotypes: those that showed reduced Labyrinthula zosterae parasites when warmed vs those that showed increased L. zosterae parasites when warmed; and two seawater temperature treatments: ambient or elevated +3.2oC. Data were collected as part of a mesocosm study at the Bodega Marine Laboratory examining the independent and interactive effects of warming, host genotypic identity, and host genotypic diversity on the prevalence and intensity of infections of seagrass by the wasting disease parasite L. zosterae. These data were published in Schenck et al (2022). Related sequence data from this experiment is accessible from the National Center for Biotechnology Information (NCBI) BioProject PRJNA716355. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/883070

  5. Woods Hole Open Access Server

    Title: Quantitative PCR cell count estimates from samples of DNA extracted from seagrass wasting disease parasite, Labyrinthula zosterae from wasting disease mesocosm experiments at Bodega Marine Laboratory in July-Sept of 2015

    Dataset 2022-11-22

    Contributors:
    Subjects:
    • climate change
    • host-parasite
    • microbiome
    • seagrass
    • wasting disease
    Summary: This data set includes quantitative PCR cell count estimates from samples of DNA extracted from seagrass wasting disease parasite, Labyrinthula zosterae, cultures of known cell concentrations run with and without DNA extracted from seagrass, Zostera marina, tissue samples to test for quantitative PCR signal inhibition. Seagrass tissue samples were collected as part of a mesocosm study at the Bodega Marine Laboratory examining the independent and interactive effects of warming, host genotypic identity, and host genotypic diversity on the prevalence and intensity of infections of seagrass by the wasting disease parasite L. zosterae. These data were plotted in Schenck et al (2022) as Figure S6. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/883055

  6. Woods Hole Open Access Server

    Title: Seagrass metrics from from seagrass wasting disease mesocosm experiments conducted at Bodega Marine Laboratory from July-September 2015

    Dataset 2022-11-22

    Contributors:
    Subjects:
    • Zostera marina
    • microbiome
    • seagrass wasting disease
    • host-parasite
    • seagrass
    • wasting disease
    Summary: This dataset includes seagrass metrics (diversity, biomass, growth, and wasting disease) from mesocosm experiments at Bodega Marine Laboratory in July-September 2015. Data were collected as part of a mesocosm study at the Bodega Marine Laboratory examining the independent and interactive effects of warming, host genotypic identity, and host genotypic diversity on the prevalence and intensity of infections of seagrass by the wasting disease parasite Labyrinthula zosterae. These data were published in Schenck et al (2022). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/879749

  7. Woods Hole Open Access Server

    Title: Temperature from seagrass wasting disease mesocosm experiments at Bodega Marine Laboratory in June-July 2015

    Dataset 2022-11-22

    Contributors:
    Subjects:
    • climate change
    • host-parasite
    • microbiome
    • seagrass
    • wasting disease
    Summary: This dataset includes seawater temperature measurements from mesocosms. Data were collected as part of a mesocosm study at the Bodega Marine Laboratory examining the independent and interactive effects of warming, host genotypic identity, and host genotypic diversity on the prevalence and intensity of infections of seagrass by the wasting disease parasite Labyrinthula zosterae. These data were plotted in Schenck et al (2022) as Figure S1. And Bois et al., 2021 as Figure 1. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/883037

  8. Woods Hole Open Access Server

    Title: Particulate organic carbon from the formation fluids recovered from the CORKs installed at North Pond; collected on Maria S. Merian cruise MSM20-5 in 2012

    Dataset 2022-05-13

    Contributors:
    Summary: This dataset includes particulate organic carbon from the formation fluids recovered from the CORKs installed at North Pond; collected on Maria S. Merian cruise MSM20-5 in 2012. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/630335

  9. Woods Hole Open Access Server

    Title: Analyses of nitrate reference solutions in 18O-labeled water with the denitrifier method (Biological Nitrogen Isotope Fractionation project)

    Dataset 2022-01-14

    Contributors:
    Summary: IAEA-NO3 and USGS-34 reference solutions were supplemented with 18O-labeled water and analyzed for N and O isotope ratios. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/865519

  10. Woods Hole Open Access Server

    Title: Volume effects on blanks originating from the bacterial concentrates, equilibration with atmospheric N2O, and NO3- contamination of the water into which the standards were diluted from 2017-2020 (Biological Nitrogen Isotope Fractionation project)

    Dataset 2022-01-14

    Contributors:
    Summary: Volume-dependent N2O blanks originating from the bacterial concentrates, equilibration with atmospheric N2O, and NO3- contamination of the water into which the standards were diluted. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/865089

  11. Woods Hole Open Access Server

    Title: Comparison of Membrane Inlet Mass Spectrometry (MIMS) to Isotope Ratio Mass Spectrometer (IRMS)

    Dataset 2019-10-02

    Contributors:
    Summary: In order to ensure that 15N2 atom% effectuated by Membrane Inlet Mass Spectrometry, we tested whether the mass-specific signal ratios returned by MIMS are equivalent with parallel measurements on a Isotope Ratio Mass Spectrometer, on the basis that the latter returns accurate ratios (see 778000 cal_iso). MIMS and IRMS returned identical values for parallel samples. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/778065

  12. Woods Hole Open Access Server

    Title: Analysis of dissolved 15N2 gas standards by Membrane Inlet Mass Spectrometry

    Dataset 2019-10-02

    Contributors:
    Summary: In order to verify that measurements of the 15N2 atom% of dissolved N2 gas samples effectuated by Membrane Inlet Mass Spectrometry are accurate, we developed a specific protocol to prepare dissolved 15N2 gas standards. We detail the protocol herein, and report representative MIMS measurements of the prepared standards. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/778021

  13. Woods Hole Open Access Server

    Title: The acetate and inorganic carbon uptake rates as determined via stable isotopic tracers from Maria S. Merian cruise MSM20-5 in 2012; data generated using the formation fluids recovered from CORKs installed at North Pond

    Dataset 2022-05-13

    Contributors:
    Summary: This dataset includes the acetate and inorganic carbon uptake rates as determined via stable isotopic tracers from Maria S. Merian cruise MSM20-5 in 2012; data were generated using the formation fluids recovered from CORKs installed at North Pond. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/637804

  14. Woods Hole Open Access Server

    Title: High throughput tag-sequencing data from Gorda Ridge Hydrothermal vent field, including 16S and 18S rRNA gene sequences, and environmental metadata from Gorda Ridge Seamount, May/June 2019

    Dataset 2021-01-06

    Contributors:
    Summary: High throughput tag-sequencing data from Gorda Ridge Hydrothermal vent field, including 16S and 18S rRNA gene sequences, and environmental metadata from Gorda Ridge Seamount, May/June 2019. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/828392

  15. Woods Hole Open Access Server

    Title: Sponge volume at Virgin Islands Territorial Coral Reef Monitoring Program’s (TCRMP) permanent monitoring sites, 2015-2017

    Dataset 2020-07-08

    Contributors:
    Summary: Sponge volume at Virgin Islands Territorial Coral Reef Monitoring Program’s (TCRMP) permanent monitoring sites, 2015-2017. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/814490

  16. Woods Hole Open Access Server

    Title: Trial A test of the dissolution method for estimates of the 15N2 atom% of incubations

    Dataset 2019-10-02

    Contributors:
    Summary: The “dissolution” method to measure N2 fixation rates with 15N2 gas tracer involves the preparation of 15N2-enriched water that is then added to each incubation bottle. Investigators typically measure the 15N2 atom% of the 15N2-enriched inoculum by MIMS, and extrapolate the 15N2 atom% in the incubations based on the inoculum value. Here, we demonstrate that such extrapolation yields inaccurate estimates of the 15N2 atom% of incubations. The latter should be measured directly. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/778126

  17. Woods Hole Open Access Server

    Title: Test of integrity of dissolved 15N2 gas samples stored in Exetainer vials

    Dataset 2019-10-02

    Contributors:
    Summary: We monitored the 15N2 gas atom% values of prepared solutions stored in Exetainer vials (filled with no headspace) in order to verify that these values remained stable over a period of weeks to months of storage. The integrity of samples was preserved for at least 6 months. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/778047

  18. Woods Hole Open Access Server

    Title: Reconstructed genomes from North Pond, western flank of the Mid-Atlantic Ridge, from 2012-2014

    Dataset 2019-12-02

    Contributors:
    Summary: Reconstructed genomes from North Pond For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/782058

  19. Woods Hole Open Access Server

    Title: Net oxygen consumption rates of the fluids recovered from the CORKs installed at North Pond; collected on Maria S. Merian cruise MSM37 in 2014

    Dataset 2022-05-13

    Contributors:
    Summary: This dataset includes net oxygen consumption rates of the fluids recovered from the CORKs installed at North Pond; collected on Maria S. Merian cruise MSM37 in 2014. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/630314

  20. Woods Hole Open Access Server

    Title: DOC, POC, d13C-POC, PN from a diffuse vent in West Mata sampled in May 2009 using ROV Jason II deployed from R/V Thomas Thompson.

    Dataset 2021-04-15

    Contributors:
    Subjects:
    • Dissolved Organic Carbon
    • DOC
    • Dissolved organic nitrogen
    • DON
    • Particulate organic carbon
    • POC
    • Stable carbon isotopes
    • Nitrate
    • Ammonium
    Summary: DOC, POC, d13C-POC, PN from a diffuse vent in West Mata sampled in May 2009 using ROV Jason II deployed from R/V Thomas Thompson. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/844580