http://lod.bco-dmo.org/id/dataset/893256 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 2023-04-05 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Ruegeria pomeroyi RB-TnSeq Transponson Mutant Library Screen Experimental Data February 2021 (C-CoMP Marine Bacterial Transporters project) 2023-04-05 publication 2023-04-05 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2023-05-24 publication https://doi.org/10.26008/1912/bco-dmo.893256.1 Mary Ann Moran University of Georgia principalInvestigator Christopher R. Reisch University of Florida principalInvestigator Catalina Mejia University of Florida principalInvestigator Lidimarie Trujillo Rodriguez University of Florida 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., Reisch, C. R., Mejia, C., Trujillo Rodriguez, L. (2023) Ruegeria pomeroyi RB-TnSeq Transponson Mutant Library Screen Experimental Data February 2021 (C-CoMP Marine Bacterial Transporters project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-04-05 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.893256.1 [access date] 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 Funding provided by Simons Foundation (Simons) Award Number: 542391 completed Mary Ann Moran University of Georgia 706-542-6481 Department of Marine Sciences Athens GA 30602 USA mmoran@uga.edu pointOfContact Christopher R. Reisch University of Florida Dept. of Microbiology and Cell Science University of Florida Gainesville FL 32611 USA creisch@ufl.edu pointOfContact Catalina Mejia University of Florida Dept. of Microbiology and Cell Science University of Florida Gainesville FL 32611 USA catalinamejia@ufl.edu pointOfContact Lidimarie Trujillo Rodriguez University of Florida Dept. of Microbiology and Cell Science University of Florida Gainesville FL 32611 USA ltrujillo@ufl.edu pointOfContact asNeeded Dataset Version: 1 Unknown Locus ID T0_1 T0_2 T0_3 T0_4 Cysteate_1 Cysteate_2 Cysteate_3 Cysteate_4 DMSP_1 DMSP_2 DMSP_3 DMSP_4 DHPS_1 DHPS_2 DHPS_3 DHPS_4 Leucine_1 Leucine_2 Leucine_3 Leucine_4 Arginine_1 Arginine_2 Arginine_3 Arginine_4 Ectoine_1 Ectoine_2 Ectoine_3 Ectoine_4 GlcNAc_1 GlcNAc_2 GlcNAc_3 GlcNAc_4 Glucose_1 Glucose_2 Glucose_3 Glucose_4 Xylose_1 Xylose_2 Xylose_3 Xylose_4 Glycolate_1 Glycolate_2 Glycolate_3 Glycolate_4 Phenylacetate_1 Phenylacetate_2 Phenylacetate_3 Phenylacetate_4 Malate_1 Malate_2 Malate_3 Malate_4 3-Hydoxybutyrate_1 3-Hydoxybutyrate_2 3-Hydoxybutyrate_3 3-Hydoxybutyrate_4 Acetate_1 Acetate_2 Acetate_3 Acetate_4 Spermidine_1 Spermidine_2 Spermidine_3 Spermidine_4 Threonine_1 Threonine_2 Threonine_3 Threonine_4 Tyramine_1 Tyramine_2 Tyramine_3 Tyramine_4 Gluconate_1 Gluconate_2 Gluconate_3 Gluconate_4 Serine_1 Serine_2 Serine_3 Serine_4 Glycine_1 Glycine_2 Glycine_3 Glycine_4 Ribose_1 Ribose_2 Ribose_3 Ribose_4 Proline_1 Proline_2 Proline_3 Proline_4 IAM_1 IAM_2 IAM_3 IAM_4 NextSeq SE150 (Illumina, San Diego, CA, USA) Synergy H1 plate reader (BioTek, Winooski, VT, USA) theme None, User defined Site_ID sample time replicate featureType BCO-DMO Standard Parameters Automated DNA Sequencer plate reader 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 Function and Importance of Marine Bacterial Transporters of Plankton Exometabolites https://osprey.bco-dmo.org/project/884792 Function and Importance of Marine Bacterial Transporters of Plankton Exometabolites <p><strong>Project:</strong></p> <p>Observing expression of marine bacterial transporter systems with transcriptomic or proteomic tools can provide valuable information about the metabolomic environment. However, these ‘omics approaches are limited by the low rate of transporter gene annotation. Here, a barcoded, arrayed, mutant library of the marine bacterium <em>Ruegeria pomeroyi</em> DSS-3 is employed in high throughput screens to identify the target substrates of 13 transporter systems. A set of 156 isolated putative transporter mutants were screened for growth on minimal medium with 63 substrates, each as a sole carbon source. Mutants that demonstrated a growth defect on a specific substrate were selected for secondary, higher resolution, growth screening. Mutants that continued to demonstrate growth defect relative to the pooled-mutant library (pooled-BarSeq, used as an analog for wildtype) were screened for their ability to drawdown the target substate. Gene annotations were made when mutants of the given transporter demonstrated both growth and drawdown defects on the target substrate.</p> <p>In addition to the isolated mutant screens, the pooled barcoded transposon mutant library (pooled-BarSeq) was grown on minimal medium with selected substrates, each as sole carbon source, such that the relative enrichment or depletion of each mutant could demonstrate its fitness cost associated with the loss of each disrupted gene when grown on each substrate. The results of pooled-BarSeq screens had mixed consistency with the isolated mutant screens, demonstrating the value of isolated mutants for transporter annotation.</p> <p><strong>Program:</strong></p> <p>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.</p> C-CoMP Marine Bacterial Transporters largerWorkCitation project eng; USA oceans 2021-02-01 2021-02-28 0 BCO-DMO catalogue of parameters from Ruegeria pomeroyi RB-TnSeq Transponson Mutant Library Screen Experimental Data February 2021 (C-CoMP Marine Bacterial Transporters 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 http://lod.bco-dmo.org/id/dataset-parameter/894617.rdf Name: Locus ID Units: unitless Description: <p>Locus ID of a gene in the Ruegeria pomeroyi DSS-3 genome.</p> http://lod.bco-dmo.org/id/dataset-parameter/894618.rdf Name: T0_1 Units: hours Description: <p>Time 0 replicate 1</p> http://lod.bco-dmo.org/id/dataset-parameter/894619.rdf Name: T0_2 Units: hours Description: <p>Time 0 replicate 2</p> http://lod.bco-dmo.org/id/dataset-parameter/894620.rdf Name: T0_3 Units: hours Description: <p>Time 0 replicate 3</p> http://lod.bco-dmo.org/id/dataset-parameter/894621.rdf Name: T0_4 Units: hours Description: <p>Time 0 replicate 4</p> http://lod.bco-dmo.org/id/dataset-parameter/894622.rdf Name: Cysteate_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on Cysteate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894623.rdf Name: Cysteate_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on Cysteate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894624.rdf Name: Cysteate_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on Cysteate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894625.rdf Name: Cysteate_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on Cysteate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894626.rdf Name: DMSP_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on DMSP.</p> http://lod.bco-dmo.org/id/dataset-parameter/894627.rdf Name: DMSP_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on DMSP.</p> http://lod.bco-dmo.org/id/dataset-parameter/894628.rdf Name: DMSP_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on DMSP.</p> http://lod.bco-dmo.org/id/dataset-parameter/894629.rdf Name: DMSP_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on DMSP.</p> http://lod.bco-dmo.org/id/dataset-parameter/894630.rdf Name: DHPS_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on DHPS.</p> http://lod.bco-dmo.org/id/dataset-parameter/894631.rdf Name: DHPS_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on DHPS.</p> http://lod.bco-dmo.org/id/dataset-parameter/894632.rdf Name: DHPS_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on DHPS.</p> http://lod.bco-dmo.org/id/dataset-parameter/894633.rdf Name: DHPS_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on DHPS.</p> http://lod.bco-dmo.org/id/dataset-parameter/894634.rdf Name: Leucine_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on Leucine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894635.rdf Name: Leucine_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on Leucine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894636.rdf Name: Leucine_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on Leucine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894637.rdf Name: Leucine_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on Leucine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894638.rdf Name: Arginine_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on Arginine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894639.rdf Name: Arginine_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on Arginine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894640.rdf Name: Arginine_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on Arginine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894641.rdf Name: Arginine_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on Arginine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894642.rdf Name: Ectoine_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on Ectoine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894643.rdf Name: Ectoine_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on Ectoine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894644.rdf Name: Ectoine_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on Ectoine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894645.rdf Name: Ectoine_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on Ectoine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894646.rdf Name: GlcNAc_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on GlcNAc.</p> http://lod.bco-dmo.org/id/dataset-parameter/894647.rdf Name: GlcNAc_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on GlcNAc.</p> http://lod.bco-dmo.org/id/dataset-parameter/894648.rdf Name: GlcNAc_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on GlcNAc.</p> http://lod.bco-dmo.org/id/dataset-parameter/894649.rdf Name: GlcNAc_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on GlcNAc.</p> http://lod.bco-dmo.org/id/dataset-parameter/894650.rdf Name: Glucose_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on Glucose.</p> http://lod.bco-dmo.org/id/dataset-parameter/894651.rdf Name: Glucose_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on Glucose.</p> http://lod.bco-dmo.org/id/dataset-parameter/894652.rdf Name: Glucose_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on Glucose.</p> http://lod.bco-dmo.org/id/dataset-parameter/894653.rdf Name: Glucose_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on Glucose.</p> http://lod.bco-dmo.org/id/dataset-parameter/894654.rdf Name: Xylose_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on Xylose.</p> http://lod.bco-dmo.org/id/dataset-parameter/894655.rdf Name: Xylose_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on Xylose.</p> http://lod.bco-dmo.org/id/dataset-parameter/894656.rdf Name: Xylose_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on Xylose.</p> http://lod.bco-dmo.org/id/dataset-parameter/894657.rdf Name: Xylose_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on Xylose.</p> http://lod.bco-dmo.org/id/dataset-parameter/894658.rdf Name: Glycolate_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on Glycolate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894659.rdf Name: Glycolate_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on Glycolate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894660.rdf Name: Glycolate_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on Glycolate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894661.rdf Name: Glycolate_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on Glycolate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894662.rdf Name: Phenylacetate_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on Phenylacetate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894663.rdf Name: Phenylacetate_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on Phenylacetate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894664.rdf Name: Phenylacetate_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on Phenylacetate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894665.rdf Name: Phenylacetate_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on Phenylacetate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894666.rdf Name: Malate_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on Malate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894667.rdf Name: Malate_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on Malate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894668.rdf Name: Malate_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on Malate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894669.rdf Name: Malate_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on Malate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894670.rdf Name: 3-Hydoxybutyrate_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on 3-Hydroxybutyrate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894671.rdf Name: 3-Hydoxybutyrate_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on 3-Hydroxybutyrate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894672.rdf Name: 3-Hydoxybutyrate_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on 3-Hydroxybutyrate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894673.rdf Name: 3-Hydoxybutyrate_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on 3-Hydroxybutyrate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894674.rdf Name: Acetate_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on Acetate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894675.rdf Name: Acetate_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on Acetate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894676.rdf Name: Acetate_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on Acetate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894677.rdf Name: Acetate_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on Acetate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894678.rdf Name: Spermidine_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on Spermidine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894679.rdf Name: Spermidine_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on Spermidine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894680.rdf Name: Spermidine_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on Spermidine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894681.rdf Name: Spermidine_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on Spermidine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894682.rdf Name: Threonine_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on Threonine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894683.rdf Name: Threonine_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on Threonine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894684.rdf Name: Threonine_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on Threonine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894685.rdf Name: Threonine_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on Threonine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894686.rdf Name: Tyramine_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on Tyramine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894687.rdf Name: Tyramine_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on Tyramine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894688.rdf Name: Tyramine_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on Tyramine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894689.rdf Name: Tyramine_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on Tyramine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894690.rdf Name: Gluconate_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on Gluconate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894691.rdf Name: Gluconate_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on Gluconate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894692.rdf Name: Gluconate_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on Gluconate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894693.rdf Name: Gluconate_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on Gluconate.</p> http://lod.bco-dmo.org/id/dataset-parameter/894694.rdf Name: Serine_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on Serine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894695.rdf Name: Serine_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on Serine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894696.rdf Name: Serine_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on Serine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894697.rdf Name: Serine_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on Serine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894698.rdf Name: Glycine_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on Glycine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894699.rdf Name: Glycine_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on Glycine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894700.rdf Name: Glycine_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on Glycine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894701.rdf Name: Glycine_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on Glycine.</p> http://lod.bco-dmo.org/id/dataset-parameter/894702.rdf Name: Ribose_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on Ribose.</p> http://lod.bco-dmo.org/id/dataset-parameter/894703.rdf Name: Ribose_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on Ribose.</p> http://lod.bco-dmo.org/id/dataset-parameter/894704.rdf Name: Ribose_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on Ribose.</p> http://lod.bco-dmo.org/id/dataset-parameter/894705.rdf Name: Ribose_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on Ribose.</p> http://lod.bco-dmo.org/id/dataset-parameter/894706.rdf Name: Proline_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on Proline.</p> http://lod.bco-dmo.org/id/dataset-parameter/894707.rdf Name: Proline_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on Proline.</p> http://lod.bco-dmo.org/id/dataset-parameter/894708.rdf Name: Proline_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on Proline.</p> http://lod.bco-dmo.org/id/dataset-parameter/894709.rdf Name: Proline_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on Proline.</p> http://lod.bco-dmo.org/id/dataset-parameter/894710.rdf Name: IAM_1 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 1 sample grown on IAM.</p> http://lod.bco-dmo.org/id/dataset-parameter/894711.rdf Name: IAM_2 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 2 sample grown on IAM.</p> http://lod.bco-dmo.org/id/dataset-parameter/894712.rdf Name: IAM_3 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 3 sample grown on IAM.</p> http://lod.bco-dmo.org/id/dataset-parameter/894713.rdf Name: IAM_4 Units: Number of sequence counts (barcodes) that mapped to each gene in the treatment. Description: <p>Replicate 4 sample grown on IAM.</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 1038440 https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/8c7147b2-6268-4201-8737-0ac1b43e562b/content download https://doi.org/10.26008/1912/bco-dmo.893256.1 download onLine dataset &lt;p&gt;&lt;strong&gt;Processing Notes from Researcher:&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;Sequence data were processed according to Wetmore et al (2015). Following quality control, an average of 35,090 unique barcodes mapped to insertions that fell within the interior 10 to 90% of&amp;nbsp;&lt;em&gt;R. pomeroyi&amp;nbsp;&lt;/em&gt;coding sequences. In total, 55 million reads were mapped to insertions in 3,570 genes (out of 4,469 protein-encoding genes in the&amp;nbsp;&lt;em&gt;R. pomeroyi&lt;/em&gt;&amp;nbsp;genome) with a median of 404,513 mapped reads per sample. Reads mapping to different insertion sites within the same coding sequence were pooled.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;BCO-DMO Processing Notes:&lt;/strong&gt;&lt;/p&gt; &lt;ul&gt; &lt;li&gt;Removed spaces and special characters from column header names (replaced with underscores &quot;_&quot;)&lt;/li&gt; &lt;/ul&gt; &lt;div class=&quot;field&quot; id=&quot;form_data_processing&quot;&gt; &lt;p&gt;&amp;nbsp;&lt;/p&gt; &lt;/div&gt; &lt;div class=&quot;field&quot; id=&quot;form_problems&quot;&gt;&amp;nbsp;&lt;/div&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 NextSeq SE150 (Illumina, San Diego, CA, USA) NextSeq SE150 (Illumina, San Diego, CA, USA) PI Supplied Instrument Name: NextSeq SE150 (Illumina, San Diego, CA, USA) PI Supplied Instrument Description:An aliquot of 8 ng of product from each sample was pooled, purified using HiPrep beads (MagBio, Gaithersburg, MD, USA), and sequenced on a NextSeq SE150 Mid Output flow cell (SE150) at the Georgia Genomics and Bioinformatics Core Facility (Athens, Georgia, 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. Synergy H1 plate reader (BioTek, Winooski, VT, USA) Synergy H1 plate reader (BioTek, Winooski, VT, USA) PI Supplied Instrument Name: Synergy H1 plate reader (BioTek, Winooski, VT, USA) PI Supplied Instrument Description:After growth with shaking at 25oC for 72 h in a Synergy H1 plate reader (BioTek, Winooski, VT, USA) , cultures were serially transferred into fresh media four times and then transferred to 1.5 ml tubes, pelleted by centrifugation at 8,000 x g for 3 min, and stored at -80oC until further processing. Instrument Name: plate reader Instrument Short Name: Instrument Description: Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.