http://lod.bco-dmo.org/id/dataset/818765
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
2020-07-16
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Transcriptome data for bacteria collected eight hours after individual inoculation into a diatom Thalassiosira psuedonana culture
2020-07-16
publication
2020-07-16
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-07-20
publication
https://doi.org/10.26008/1912/bco-dmo.818765.1
Mary Ann Moran
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. (2020) Transcriptome data for bacteria collected eight hours after individual inoculation into a diatom Thalassiosira psuedonana culture. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-07-16 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.818765.1 [access date]
NCBI accessions Dataset Description: <p>Transcriptome data for bacteria Ruegeria pomeroyi DSS-3, Stenotrophomonas sp. SKA14, Polaribacter dokdonensis MED152, and Dokdonia MED134 collected eight hours after individual inoculation into a diatom Thalassiosira psuedonana culture. The sequence data description for PRHNA448168 is at https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA448168.</p> Methods and Sampling: <p>Thalassiosira pseudonana were removed from the co-cultures by pre-filtration through 2.0 µm pore-size filters, and bacteria were collected on 0.2 µm pore-size filters. Filters were incubated in SDS (0.6% final concentration) and proteinase K (120 ng μl –1 final concentration). RNA was extracted from duplicates of each treatment by adding an equal volume of acid phenol:chloroform:isoamyl-alcohol, followed by shaking, centrifugation, and collection of the supernatant. A second extraction was carried out by the addition of an equal volume of chloroform:isoamyl-alcohol. RNA was recovered from the supernatant, treated to remove rRNA, and sequenced.</p>
<p>Each sequence library is from four independent bacterial samples that were pooled for sequencing. The data are assigned to one of the four samples post-sequencing by mapping to the genomes of each of the four bacteria. The data table provides the accession numbers of the bacterial genomes to be used for mapping in the final column.</p>
Funding provided by NSF Division of Integrative Organismal Systems (NSF IOS) Award Number: IOS-1656311 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1656311
completed
Mary Ann Moran
University of Georgia
706-542-6481
Department of Marine Sciences
Athens
GA
30602
USA
mmoran@uga.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_Name
NCBI_Bioproject_Accession
BioSample
Description
replicate
NCBI_Genome_Accession
taxon_microbe
HiSeq Illumina 2500
theme
None, User defined
sample identification
accession number
sample description
replicate
taxon
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
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.
Metabolic Currencies of the Ocean Carbon Cycle
https://www.bco-dmo.org/project/765521
Metabolic Currencies of the Ocean Carbon Cycle
<p><em>NSF Award Abstract:</em><br />
The roles of microbes in cycling carbon and nutrients in the ocean - the largest biological system on Earth - were initially described about 40 years ago. Now, it is known that half of Earth's primary production is carried out by marine phytoplankton, and half of that is recycled within weeks by marine bacteria. This proposal is a collaboration between microbiologists and chemists to identify the specific compounds that pass between phytoplankton and bacteria in surface ocean waters. Identifying the key chemicals of the ocean's microbial food web will provide insights into how the marine carbon cycle is regulated, generate data to improve ocean carbon models, and train new scientists at the interface of microbiology and chemistry. Hands-on learning opportunities in microbial ecology will be provided for high school students, both in the classroom and in marine ecosystems of the Georgia coast.</p>
<p>Phytoplankton metabolites that sustain the flow of carbon between microbial autotrophs and heterotrophs in the surface ocean carbon cycle will be identified in this project. A matrix of model systems consisting of bacteria-phytoplankton co-cultures will be used as biological assays for key metabolites based on expression patterns of bacterial transporter genes. The chemical identity of candidate metabolites and evaluation of their potential ecological role will be carried out by exometabolomic analysis of co-cultures with bacterial transporter mutants. Both advanced mass spectrometry and NMR will be used for metabolomics analysis, taking advantage of the sensitivity and compound identification strengths of each. The distribution of candidate metabolites in the ocean microbiome and other microbial systems will be characterized by mining environmental sequence datasets for orthologous transporter genes. This project represents a novel approach to identifying metabolites important in microbiome function, compounds often difficult to address with standard chemical approaches because of their low concentrations and high biological demand.</p>
Metabolic Currencies
largerWorkCitation
project
eng; USA
biota
oceans
2017-02-25
2017-12-31
0
BCO-DMO catalogue of parameters from Transcriptome data for bacteria collected eight hours after individual inoculation into a diatom Thalassiosira psuedonana culture
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/818789.rdf
Name: Sample_Name
Units: unitless
Description: sample identifier
http://lod.bco-dmo.org/id/dataset-parameter/818790.rdf
Name: NCBI_Bioproject_Accession
Units: unitless
Description: NCBI Bioproject accession number
http://lod.bco-dmo.org/id/dataset-parameter/818791.rdf
Name: BioSample
Units: unitless
Description: NCBI Biosample accession number
http://lod.bco-dmo.org/id/dataset-parameter/818792.rdf
Name: Description
Units: unitless
Description: Description of sample
http://lod.bco-dmo.org/id/dataset-parameter/818793.rdf
Name: replicate
Units: unitless
Description: Replicate number
http://lod.bco-dmo.org/id/dataset-parameter/818794.rdf
Name: NCBI_Genome_Accession
Units: unitless
Description: NCBI Genome accession number
http://lod.bco-dmo.org/id/dataset-parameter/818795.rdf
Name: taxon_microbe
Units: unitless
Description: Microbial identification
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
2120
https://darchive.mblwhoilibrary.org/bitstream/1912/25981/1/dataset-818765_diatom-matrix-rnaseq__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.818765.1
download
onLine
dataset
<p>Thalassiosira pseudonana were removed from the co-cultures by pre-filtration through 2.0 µm pore-size filters, and bacteria were collected on 0.2 µm pore-size filters. Filters were incubated in SDS (0.6% final concentration) and proteinase K (120 ng μl –1 final concentration). RNA was extracted from duplicates of each treatment by adding an equal volume of acid phenol:chloroform:isoamyl-alcohol, followed by shaking, centrifugation, and collection of the supernatant. A second extraction was carried out by the addition of an equal volume of chloroform:isoamyl-alcohol. RNA was recovered from the supernatant, treated to remove rRNA, and sequenced.</p>
<p>Each sequence library is from four independent bacterial samples that were pooled for sequencing. The data are assigned to one of the four samples post-sequencing by mapping to the genomes of each of the four bacteria. The data table provides the accession numbers of the bacterial genomes to be used for mapping in the final column.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing Notes:</strong><br />
- data submitted in Excel file "Diatom matrix data table.xlsx" sheet "Sheet1" extracted to csv<br />
- added conventional header with dataset name, PI name, version date<br />
-&nbsp;NCBI_Genome_Accession data were split into separate rows<br />
- Replicate number and&nbsp;Taxon were put into their own columns</p>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
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
HiSeq Illumina 2500
HiSeq Illumina 2500
PI Supplied Instrument Name: HiSeq Illumina 2500 Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.