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: &lt;p&gt;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.&lt;/p&gt; Methods and Sampling: &lt;p&gt;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.&lt;/p&gt; &lt;p&gt;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.&lt;/p&gt; Funding provided by NSF Division of Integrative Organismal Systems (NSF IOS) Award Number: IOS-1656311 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=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://osprey.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: <p>sample identifier</p> http://lod.bco-dmo.org/id/dataset-parameter/818790.rdf Name: NCBI_Bioproject_Accession Units: unitless Description: <p>NCBI Bioproject accession number</p> http://lod.bco-dmo.org/id/dataset-parameter/818791.rdf Name: BioSample Units: unitless Description: <p>NCBI Biosample accession number</p> http://lod.bco-dmo.org/id/dataset-parameter/818792.rdf Name: Description Units: unitless Description: <p>Description of sample</p> http://lod.bco-dmo.org/id/dataset-parameter/818793.rdf Name: replicate Units: unitless Description: <p>Replicate number</p> http://lod.bco-dmo.org/id/dataset-parameter/818794.rdf Name: NCBI_Genome_Accession Units: unitless Description: <p>NCBI Genome accession number</p> http://lod.bco-dmo.org/id/dataset-parameter/818795.rdf Name: taxon_microbe Units: unitless Description: <p>Microbial identification</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 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 &lt;p&gt;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.&lt;/p&gt; &lt;p&gt;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.&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;&lt;strong&gt;BCO-DMO Processing Notes:&lt;/strong&gt;&lt;br /&gt; - data submitted in Excel file &quot;Diatom matrix data table.xlsx&quot; sheet &quot;Sheet1&quot; extracted to csv&lt;br /&gt; - added conventional header with dataset name, PI name, version date&lt;br /&gt; -&amp;nbsp;NCBI_Genome_Accession data were split into separate rows&lt;br /&gt; - Replicate number and&amp;nbsp;Taxon were put into their own columns&lt;/p&gt; &lt;p&gt;&amp;nbsp;&lt;/p&gt; 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: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.