http://lod.bco-dmo.org/id/dataset/916134
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2023-12-05
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Metadata for transcriptomic expression data from cultures of Ruegeria pomeroyi DSS-3 and Alteromonas macleodii MIT1002 grown in defined culture media with either glucose, acetate, or a mix of both as carbon substrates
2023-12-06
publication
2023-12-06
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-12-12
publication
https://doi.org/10.26008/1912/bco-dmo.916134.1
Mary Ann Moran
University of Georgia
principalInvestigator
Zachary Shane Cooper
University of Georgia
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Moran, M. A., Cooper, Z. S. (2023) Metadata for transcriptomic expression data from cultures of Ruegeria pomeroyi DSS-3 and Alteromonas macleodii MIT1002 grown in defined culture media with either glucose, acetate, or a mix of both as carbon substrates. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-12-06 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.916134.1 [access date]
Substrate-specific metabolic responses of model marine bacteria - metadata for transcriptomic expression data Dataset Description: Methods and Sampling: <p>This lab study took place in Athens, Georiga (GA), USA within the Department of Marine Sciences at the University of Georgia. Experiments were conducted on several dates: samples ending in _glc_a/b/c (samples grown with glucose only) were collected February 22-23, 2022; samples ending in _ac_a/b/c (samples grown with acetate only) were collected June 24-25, 2022; and the rest of the samples ending with _glc_ac_5/8/19/34_a/b/c (grown with both glucose and acetate) were collected July 16-17, 2022.</p>
<p>Samples were collected for transcriptomic analysis during exponential growth phase from liquid cultures, and samples were pelleted and immediately frozen at -80°C. RNA was extracted from thawed samples using the Zymo Quick-RNA Fungal/Bacterial Microprep kit (Irvine, CA, USA). Ribosomal RNAs were depleted using NEBNext® rRNA Depletion Kit (Ipswich, MA, USA), and the remaining RNA was purified using the Zymo RNA Clean and Concentrator-5 kit (Irvine, CA, USA). RNA concentration was quantified using Qubit fluorometry (Invitrogen, Waltham, MA, USA), and libraries were prepped using the NEBNext® Ultra™ II Directional RNA Library Prep kit (Ipswich, MA, USA). Sequencing was conducted at the Georgia Genomics and Bioinformatics Center (Athens, GA, USA) using the Illumina NextSeq 2000 platform to obtain 50-bp single-end reads.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2019589 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2019589
completed
Mary Ann Moran
University of Georgia
706-542-6481
Department of Marine Sciences
Athens
GA
30602
USA
mmoran@uga.edu
pointOfContact
Zachary Shane Cooper
University of Georgia
Department of Marine Sciences 325 Sanford Drive
Athens
GA
30602
USA
zachary.s.cooper@gmail.com
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_Name
Accession
BioProject
Organism
Strain
Tax_ID
Glucose_initial_concentration_uM
Acetate_initial_concentration_uM
Sample_description
Illumina NextSeq 2000
Qubit Fluorometer
theme
None, User defined
sample identification
accession number
NCBI BioProject accession
taxon
treatment
sample description
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Fluorometer
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Center for Chemical Currencies of a Microbial Planet
https://ccomp-stc.org/
Center for Chemical Currencies of a Microbial Planet
Functions carried out by microscopic inhabitants of the surface ocean affect every aspect of life on our planet, regardless of distance from the coast. Ocean phytoplankton are responsible for half of the photosynthesis on Earth, the first step in a complex system that annually withdraws 50 billion metric tons of carbon from the atmosphere to sustain their growth. Of this, 25 billion metric tons participate in a rapid cycle in which biologically reactive material is released into seawater and converted back into carbon dioxide by marine bacteria within hours to days. The chemical-microbe network at the heart of this fast cycle remains poorly constrained; consequently, its primary currencies and controls remain elusive; its sensitivities to changing ocean conditions are unknown; and its responses to future climate scenarios are not predictable. The Center for Chemical Currencies of a Microbial Planet (C-CoMP) integrates research, education and knowledge transfer activities to develop a mechanistic understanding of surface ocean carbon flux within the context of a changing ocean and through increased participation in ocean sciences. C-CoMP supports science teams that merge biology, chemistry, modeling, and informatics to close long-standing knowledge gaps in the identities and dynamics of organic molecules that serve as the currencies of elemental transfer between the ocean and atmosphere. C-CoMP fosters education, outreach, and knowledge transfer activities that engage students of all ages, broaden participation in the next generation of ocean scientists, and extend novel open-science approaches into complementary academic and industrial communities. The Center framework is critical to this mission, uniquely facilitating an open exchange of experimental and computational science, methodological and conceptual challenges, and collaborations that establish integrated science and education partnerships. With expanded participation in ocean science research and ocean literacy across the US society, the next generation of ocean scientists will better reflect the diverse US population.
Climate-carbon feedbacks on the marine carbon reservoir are major uncertainties for future climate projections, and the trajectory and rate of ocean changes depend directly on microbial responses to temperature increases, ocean acidification, and other perturbations driven by climate change. C-CoMP research closes an urgent knowledge gap in the mechanisms driving carbon flow between ocean and atmosphere, with global implications for predictive climate models. The Center supports interdisciplinary science teams following open and reproducible science practices to address: (1) the chemical currencies of surface ocean carbon flux; (2) the structure and regulation of the chemical-microbe network that mediates this flux; and (3) sensitivity of the network and its feedbacks on climate. C-CoMP leverages emerging tools and technologies to tackle critical challenges in these themes, in synergy with existing ocean programs and consistent with NSF’s Big Ideas. C-CoMP education and outreach activities seek to overcome barriers to ocean literacy and diversify participation in ocean research. The Center is developing (1) initiatives to expand ocean literacy in K-12 and the broader public, (2) ocean sciences undergraduate curricula and research opportunities that provide multiple entry points into research experiences, (3) post-baccalaureate programs to transition undergraduates into graduate education and careers in ocean science, and (4) interdisciplinary graduate student and postdoctoral programs that prepare the next generation of ocean scientists. The C-CoMP team includes education faculty who evaluate the impacts of education and outreach activities and export successful STEM initiatives to the education community. C-CoMP is revolutionizing the technologies for studying chemical transformations in microbial systems to build understanding of the outsized impact of microbes on elemental cycles. Open science, cross-disciplinary collaborations, community engagement, and inclusive practices foster strategic advances in critical science problems and STEM initiatives. C-CoMP science, education, and knowledge-transfer themes are efficiently addressed through a sustained network of scientists addressing critical research challenges while broadening the workforce that will tackle multi-disciplinary problems with academic, industrial and policy partners.
This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
The Program's Data Management Plan (DMP) is available as a PDF document.
C-CoMP
largerWorkCitation
program
C-CoMP Model Bacteria Physiological Studies
https://osprey.bco-dmo.org/project/875254
C-CoMP Model Bacteria Physiological Studies
<p>The Center for Chemical Currencies of a Microbial Planet (C-CoMP) is focused on understanding how marine microorganisms determine the fate of labile carbon in the surface ocean. To study these chemical-biological dynamics across a variety of scales and in response to changing environmental conditions, the physiology of marine bacteria that drive chemical exchange must be explored in depth using a variety of microbiological, molecular biological, and integrative ’omics (e.g. proteomics, metabolomics, and genomics) methodologies. This project has been created to host data generated via these methods to investigate the physiological mechanisms underpinning the biogeochemical functions of model marine bacteria.</p>
C-CoMP Model Bacteria
largerWorkCitation
project
eng; USA
oceans
2022-02-22
2022-07-17
0
BCO-DMO catalogue of parameters from Metadata for transcriptomic expression data from cultures of Ruegeria pomeroyi DSS-3 and Alteromonas macleodii MIT1002 grown in defined culture media with either glucose, acetate, or a mix of both as carbon substrates
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/916275.rdf
Name: Sample_Name
Units: unitless
Description: <p>Name of sample used during the experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/916276.rdf
Name: Accession
Units: unitless
Description: <p>NCBI BioSample Accession Number</p>
http://lod.bco-dmo.org/id/dataset-parameter/916277.rdf
Name: BioProject
Units: unitless
Description: <p>NCBI BioProject Accession Number</p>
http://lod.bco-dmo.org/id/dataset-parameter/916278.rdf
Name: Organism
Units: unitless
Description: <p>Type of model marine bacteria used in this experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/916279.rdf
Name: Strain
Units: unitless
Description: <p>Strain number for the referenced bacteria</p>
http://lod.bco-dmo.org/id/dataset-parameter/916280.rdf
Name: Tax_ID
Units: unitless
Description: <p>NCBI Taxonomy ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/916281.rdf
Name: Glucose_initial_concentration_uM
Units: micromolar concentration
Description: <p>Initial concentration of glucose</p>
http://lod.bco-dmo.org/id/dataset-parameter/916282.rdf
Name: Acetate_initial_concentration_uM
Units: micromolar concentration
Description: <p>Initial concentration of acetate</p>
http://lod.bco-dmo.org/id/dataset-parameter/916283.rdf
Name: Sample_description
Units: unitless
Description: <p>Description of growth and collection conditions</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
4448
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/9655d5e5-9ebd-4238-b94e-8274bb22512a/content
download
https://doi.org/10.26008/1912/bco-dmo.916134.1
download
onLine
dataset
<p>This lab study took place in Athens, Georiga (GA), USA within the Department of Marine Sciences at the University of Georgia. Experiments were conducted on several dates: samples ending in _glc_a/b/c (samples grown with glucose only) were collected February 22-23, 2022; samples ending in _ac_a/b/c (samples grown with acetate only) were collected June 24-25, 2022; and the rest of the samples ending with _glc_ac_5/8/19/34_a/b/c (grown with both glucose and acetate) were collected July 16-17, 2022.</p>
<p>Samples were collected for transcriptomic analysis during exponential growth phase from liquid cultures, and samples were pelleted and immediately frozen at -80°C. RNA was extracted from thawed samples using the Zymo Quick-RNA Fungal/Bacterial Microprep kit (Irvine, CA, USA). Ribosomal RNAs were depleted using NEBNext® rRNA Depletion Kit (Ipswich, MA, USA), and the remaining RNA was purified using the Zymo RNA Clean and Concentrator-5 kit (Irvine, CA, USA). RNA concentration was quantified using Qubit fluorometry (Invitrogen, Waltham, MA, USA), and libraries were prepped using the NEBNext® Ultra™ II Directional RNA Library Prep kit (Ipswich, MA, USA). Sequencing was conducted at the Georgia Genomics and Bioinformatics Center (Athens, GA, USA) using the Illumina NextSeq 2000 platform to obtain 50-bp single-end reads.</p>
Specified by the Principal Investigator(s)
<p>The submitted data are raw RNA sequences in 50 bp reads in fastq format and are otherwise unprocessed. RNA sequences can be accessed on the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject PRJNA972985 (<a href="https://www.ncbi.nlm.nih.gov/bioproject/972985" target="_blank">https://www.ncbi.nlm.nih.gov/bioproject/972985</a>).</p>
<p>Within this dataset, transcripts from <em>Ruegeria pomeroyi</em> DSS-3 are included in the <em>Ruegeria pomeroyi</em> DSS-3 Digital Microbe data package that is currently available on the C-CoMP Zenodo Community page (doi: <a href="http://dx.doi.org/10.5281/zenodo.7888446" target="_blank">10.5281/zenodo.7888446</a>).</p>
Specified by the Principal Investigator(s)
- Imported original file "CCoMPmodelbacteria_metabolicresponses_primarydatafile.csv" into the BCO-DMO system.
- Renamed fields to comply with BCO-DMO naming conventions.
- Saved the final file as "916134_v1_transcriptomic_expression_metadata.csv".
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Illumina NextSeq 2000
Illumina NextSeq 2000
PI Supplied Instrument Name: Illumina NextSeq 2000 Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Qubit Fluorometer
Qubit Fluorometer
PI Supplied Instrument Name: Qubit Fluorometer Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/