http://lod.bco-dmo.org/id/dataset/719970 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 2017-11-27 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Transcriptional profile of marine bacterium Ruegeria pomeroyi in a three-member co-culture study 2017-11-29 publication 2017-11-29 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2020-01-14 publication https://doi.org/10.1575/1912/bco-dmo.719970.1 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. A. (2017) Transcriptional profile of marine bacterium Ruegeria pomeroyi in a three-member co-culture study. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-11-29 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.719970.1 [access date] Transcriptional profile of marine bacterium Ruegeria pomeroyi in a three-member co-culture study Dataset Description: &lt;p&gt;Transcriptional profile of marine bacterium &lt;em&gt;Ruegeria pomeroyi&lt;/em&gt; in a three-member co-culture study. This dataset contains the processed, QC'ed, normalized sequence data. The full raw data file is deposited in the NCBI BioProject database under accession PRJNA381627.&lt;/p&gt; &lt;p&gt;These data are published in table 2 of Landa et al., 2017, ISME Journal, in press.&lt;/p&gt; Methods and Sampling: &lt;p&gt;Published methodology in Landa et al., 2017, ISME Journal, in press.&lt;/p&gt; &lt;p&gt;One liter samples were filtered through 2-um polycarbonate (PC) membranes to collect bacterial cells and flash-frozen in liquid nitrogen and stored at -80C. Filters were extracted for RNA by the acid phenol:chloroform:isoamylalcohol method. Potential traces of DNA were removed using the Turbo DNA-free kit (Invitrogen, Waltham, MA, USA). Samples were tested for residual DNA by a 40-cycle PCR targeting the 16S rRNA gene of &lt;em&gt;R. pomeroyi&lt;/em&gt;. Samples were depleted of rRNA using custom probes for small and large subunit rRNA genes from all three microbes (Stewart et al., 2010)&lt;em&gt;.&lt;/em&gt; Libraries were prepared for two replicate cubitainers at 8 time points (16 samples) using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems, Wilmington, MA, USA) at the Georgia Genomics Facility (University of Georgia) and sequenced on a HiSeq Illumina 2500 at the Hudson Alpha Institute for Biotechnology (AL, USA).&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Reference cited:&lt;/strong&gt;&lt;br /&gt; Stewart FJ, Ottesen EA, DeLong EF. (2010). Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics. ISME J 4: 896–907. doi:&lt;a href=&quot;http://dx.doi.org/10.1038/ismej.2010.18&quot; target=&quot;_blank&quot;&gt;10.1038/ismej.2010.18&lt;/a&gt;&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1342694 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1342694 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 Locus_Tag Description Day7_R1 Day7_R2 Day9_R1 Day9_R2 Day12_R1 Day12_R2 Day15_R1 Day15_R2 Day18_R1 Day18_R2 Day23_R1 Day23_R2 Day30_R1 Day30_R2 Day37_R1 Day37_R2 HiSeq Illumina 2500 theme None, User defined sample identification brief description count 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. Dimensions of Biodiversity http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503446 Dimensions of Biodiversity (adapted from the NSF Synopsis of Program) Dimensions of Biodiversity is a program solicitation from the NSF Directorate for Biological Sciences. FY 2010 was year one of the program.  [MORE from NSF] The NSF Dimensions of Biodiversity program seeks to characterize biodiversity on Earth by using integrative, innovative approaches to fill rapidly the most substantial gaps in our understanding. The program will take a broad view of biodiversity, and in its initial phase will focus on the integration of genetic, taxonomic, and functional dimensions of biodiversity. Project investigators are encouraged to integrate these three dimensions to understand the interactions and feedbacks among them. While this focus complements several core NSF programs, it differs by requiring that multiple dimensions of biodiversity be addressed simultaneously, to understand the roles of biodiversity in critical ecological and evolutionary processes. Dimensions of Biodiversity largerWorkCitation program Bacterial Taxa that Control Sulfur Flux from the Ocean to the Atmosphere https://osprey.bco-dmo.org/project/541255 Bacterial Taxa that Control Sulfur Flux from the Ocean to the Atmosphere <p>Surface ocean bacterioplankton preside over a divergence point in the marine sulfur cycle where the fate of dimethylsulfoniopropionate (DMSP) is determined. While it is well recognized that this juncture influences the fate of sulfur in the ocean and atmosphere, its regulation by bacterioplankton is not yet understood. Based on recent findings in biogeochemistry, bacterial physiology, bacterial genetics, and ocean instrumentation, the microbial oceanography community is poised to make major advances in knowledge of this control point. This research project is ascertaining how the major taxa of bacterial DMSP degraders in seawater regulate DMSP transformations, and addresses the implications of bacterial functional, genetic, and taxonomic diversity for global sulfur cycling.</p> <p>The project is founded on the globally important function of bacterial transformation of the ubiquitous organic sulfur compound DMSP in ocean surface waters. Recent genetic discoveries have identified key genes in the two major DMSP degradation pathways, and the stage is now set to identify the factors that regulate gene expression to favor one or the other pathway during DMSP processing. The taxonomy of the bacteria mediating DMSP cycling has been deduced from genomic and metagenomic sequencing surveys to include four major groups of surface ocean bacterioplankton. How regulation of DMSP degradation differs among these groups and maps to phylogeny in co-occurring members is key information for understanding the marine sulfur cycle and predicting its function in a changing ocean. Using model organism studies, microcosm experiments (at Dauphin Island Sea Lab, AL), and time-series field studies with an autonomous sample collection instrument (at Monterey Bay, CA), this project is taking a taxon-specific approach to decipher the regulation of bacterial DMSP degradation.</p> <p>This research addresses fundamental questions of how the diversity of microbial life influences the geochemical environment of the oceans and atmosphere, linking the genetic basis of metabolic potential to taxonomic diversity. The project is training graduate students and post-doctoral scholars in microbial biodiversity and providing research opportunities and mentoring for undergraduate students. An outreach program is enhance understanding of the role and diversity of marine microorganisms in global elemental cycles among high school students. Advanced Placement Biology students are participating in marine microbial research that covers key learning goals in the AP Biology curriculum. Two high school students are selected each year for summer research internships in PI laboratories.</p> OceanSulfurFluxBact largerWorkCitation project eng; USA biota oceans 2017-11-29 0 BCO-DMO catalogue of parameters from Transcriptional profile of marine bacterium Ruegeria pomeroyi in a three-member co-culture study 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/720149.rdf Name: Locus_Tag Units: unitless Description: <p>gene identifier</p> http://lod.bco-dmo.org/id/dataset-parameter/720150.rdf Name: Description Units: unitless Description: <p>gene function, if known</p> http://lod.bco-dmo.org/id/dataset-parameter/720151.rdf Name: Day7_R1 Units: TPM (transcripts per million) Description: <p>Transcript count by day and replicate: day 7, replicate 1</p> http://lod.bco-dmo.org/id/dataset-parameter/720152.rdf Name: Day7_R2 Units: TPM (transcripts per million) Description: <p>Transcript count by day and replicate: day 7, replicate 2</p> http://lod.bco-dmo.org/id/dataset-parameter/720153.rdf Name: Day9_R1 Units: TPM (transcripts per million) Description: <p>Transcript count by day and replicate: day 9, replicate 1</p> http://lod.bco-dmo.org/id/dataset-parameter/720154.rdf Name: Day9_R2 Units: TPM (transcripts per million) Description: <p>Transcript count by day and replicate: day 9, replicate 2</p> http://lod.bco-dmo.org/id/dataset-parameter/720155.rdf Name: Day12_R1 Units: TPM (transcripts per million) Description: <p>Transcript count by day and replicate: day 12, replicate 1</p> http://lod.bco-dmo.org/id/dataset-parameter/720156.rdf Name: Day12_R2 Units: TPM (transcripts per million) Description: <p>Transcript count by day and replicate: day 12, replicate 2</p> http://lod.bco-dmo.org/id/dataset-parameter/720157.rdf Name: Day15_R1 Units: TPM (transcripts per million) Description: <p>Transcript count by day and replicate: day 15, replicate 1</p> http://lod.bco-dmo.org/id/dataset-parameter/720158.rdf Name: Day15_R2 Units: TPM (transcripts per million) Description: <p>Transcript count by day and replicate: day 15, replicate 2</p> http://lod.bco-dmo.org/id/dataset-parameter/720159.rdf Name: Day18_R1 Units: TPM (transcripts per million) Description: <p>Transcript count by day and replicate: day 18, replicate 1</p> http://lod.bco-dmo.org/id/dataset-parameter/720160.rdf Name: Day18_R2 Units: TPM (transcripts per million) Description: <p>Transcript count by day and replicate: day 18, replicate 2</p> http://lod.bco-dmo.org/id/dataset-parameter/720161.rdf Name: Day23_R1 Units: TPM (transcripts per million) Description: <p>Transcript count by day and replicate: day 23, replicate 1</p> http://lod.bco-dmo.org/id/dataset-parameter/720162.rdf Name: Day23_R2 Units: TPM (transcripts per million) Description: <p>Transcript count by day and replicate: day 23, replicate 2</p> http://lod.bco-dmo.org/id/dataset-parameter/720163.rdf Name: Day30_R1 Units: TPM (transcripts per million) Description: <p>Transcript count by day and replicate: day 30, replicate 1</p> http://lod.bco-dmo.org/id/dataset-parameter/720164.rdf Name: Day30_R2 Units: TPM (transcripts per million) Description: <p>Transcript count by day and replicate: day 30, replicate 2</p> http://lod.bco-dmo.org/id/dataset-parameter/720165.rdf Name: Day37_R1 Units: TPM (transcripts per million) Description: <p>Transcript count by day and replicate: day 37, replicate 1</p> http://lod.bco-dmo.org/id/dataset-parameter/720166.rdf Name: Day37_R2 Units: TPM (transcripts per million) Description: <p>Transcript count by day and replicate: day 37, replicate 2</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 654335 https://darchive.mblwhoilibrary.org/bitstream/1912/25145/1/dataset-719970_switch-rnaseq__v1.tsv download https://doi.org/10.1575/1912/bco-dmo.719970.1 download onLine dataset &lt;p&gt;Published methodology in Landa et al., 2017, ISME Journal, in press.&lt;/p&gt; &lt;p&gt;One liter samples were filtered through 2-um polycarbonate (PC) membranes to collect bacterial cells and flash-frozen in liquid nitrogen and stored at -80C. Filters were extracted for RNA by the acid phenol:chloroform:isoamylalcohol method. Potential traces of DNA were removed using the Turbo DNA-free kit (Invitrogen, Waltham, MA, USA). Samples were tested for residual DNA by a 40-cycle PCR targeting the 16S rRNA gene of &lt;em&gt;R. pomeroyi&lt;/em&gt;. Samples were depleted of rRNA using custom probes for small and large subunit rRNA genes from all three microbes (Stewart et al., 2010)&lt;em&gt;.&lt;/em&gt; Libraries were prepared for two replicate cubitainers at 8 time points (16 samples) using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems, Wilmington, MA, USA) at the Georgia Genomics Facility (University of Georgia) and sequenced on a HiSeq Illumina 2500 at the Hudson Alpha Institute for Biotechnology (AL, USA).&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Reference cited:&lt;/strong&gt;&lt;br /&gt; Stewart FJ, Ottesen EA, DeLong EF. (2010). Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics. ISME J 4: 896–907. doi:&lt;a href=&quot;http://dx.doi.org/10.1038/ismej.2010.18&quot; target=&quot;_blank&quot;&gt;10.1038/ismej.2010.18&lt;/a&gt;&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;Sequence quality control was performed using the FASTX toolkit, imposing a minimum quality score of 20 over 80% of read length. Reads aligning to an in-house rRNA database were removed (blastn, score cutoff&amp;nbsp;greater than or equal to 50). Remaining reads were mapped to the &lt;em&gt;R. pomeroyi&lt;/em&gt; genome (Bowtie 2; Langmead and Salzberg, 2012) and counted (HTSeq; Anders et al., 2015). Counts were converted to transcripts per million (TPM, Table S2) and data were also deposited in the NCBI BioProject database under accession PRJNA381627.&amp;nbsp;Genes with differential expression between selected time points were determined with DESeq2 (Love et al., 2014), and linear relationships of gene expression with phytoplankton abundance with Pearson correlations.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;References cited:&lt;/strong&gt;&lt;br /&gt; Langmead B, Salzberg SL. (2012). Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357–359. doi:&lt;a href=&quot;http://dx.doi.org/10.1038/nmeth.1923&quot; target=&quot;_blank&quot;&gt;10.1038/nmeth.1923&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Anders S, Pyl PT, Huber W. (2015). HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31: 166–169. doi:&lt;a href=&quot;http://dx.doi.org/10.1093/bioinformatics/btu638&quot; target=&quot;_blank&quot;&gt;10.1093/bioinformatics/btu638&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Love MI, Huber W, Anders S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15: 550. doi:&lt;a href=&quot;http://dx.doi.org/10.1186/s13059-014-0550-8&quot; target=&quot;_blank&quot;&gt;10.1186/s13059-014-0550-8&lt;/a&gt;&lt;/p&gt; &lt;p&gt;&lt;strong&gt;BCO-DMO Processing:&lt;/strong&gt;&lt;br /&gt; - modified parameter names to conform with BCO-DMO naming conventions;&lt;br /&gt; - replaced spaces with underscores in Description column.&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 PI Supplied Instrument Description:Transcripts were sequenced on a HiSeq Illumina 2500 at the Hudson Alpha Institute for Biotechnology (AL, USA). 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.