http://lod.bco-dmo.org/id/dataset/997637 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 2026-04-28 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) NCBI accession metadata for transcriptomic expression sequences run from cultures of Alteromonas macleodii MIT1002 grown with bacterial extracellular vesicles as a carbon source 2026-04-28 publication 2026-04-28 revision BCO-DMO Linked Data URI 2026-04-28 creation http://lod.bco-dmo.org/id/dataset/997637 Steven Biller Wellesley College principalInvestigator Krista Longnecker Woods Hole Oceanographic Institution principalInvestigator Ashley Stein Wellesley College 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: Biller, S., Longnecker, K., Stein, A. (2026) NCBI accession metadata for transcriptomic expression sequences run from cultures of Alteromonas macleodii MIT1002 grown with bacterial extracellular vesicles as a carbon source. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-04-28 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/997637 [access date] Alteromonas MIT1002 EV Transcriptome Dataset Description: Methods and Sampling: &lt;p&gt;This lab experiment was conducted at Wellesley College, Welleslsey MA in August 2024. &lt;em&gt;Alteromonas macleodii &lt;/em&gt;MIT1002 were grown at 24 °C in a natural seawater-based media containing 0.2 µM filtered, autoclaved seawater supplemented with 3 mM NH&lt;sub&gt;4&lt;/sub&gt;Cl, 50 µM NaH&lt;sub&gt;2&lt;/sub&gt;PO&lt;sub&gt;4&lt;/sub&gt;, Pro99 trace metals, and 0.01% (w/v) glucose. Overnight cultures of &lt;em&gt;Alteromonas&lt;/em&gt; were washed twice in media lacking added glucose (-C). Cultures were diluted to 5e6 cells/mL and supplemented with with either 1x PBS (negative control), &lt;em&gt;Prochlorococcus&lt;/em&gt; extracellular vesicles, &lt;em&gt;Alteromonas&lt;/em&gt; extracellular vesicles, or glucose as a carbon source, each in triplicate. Cultures were incubated at 24°C with shaking at 120 rpm.&amp;nbsp;Samples were collected at two timepoints (representing early and late exponential growth phase) by pelleting at 10,000 xg for 15 minutes, flash freezing on dry ice, and storing at -80 °C. Cells were resuspended and lysed in 600 µL Zymo TriReagent and RNA was extracted using the Zymo Trizol RNA Extraction RNA spin column kit following the manufacturer’s protocol. The columns were washed and treated with DNAse per manufacturers recommendation. RNA was eluted in 50 µL of RNase-free water and quantified using the Qubit RNA High Sensitivity kit (Invitrogen). Ribosomal RNA was depleted using the Qiagen QIAseq FastSelect kit, then the Kapa RNA Hyperprep kit. Paired-end 150nt sequencing data was generated on an Illumina NovaSeq X. RNA library preparation and sequencing was carried out by the &amp;nbsp;Bauer Core Facility (Harvard University).&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2049004 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2049004 Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2044346 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2044346 onGoing Steven Biller Wellesley College 781-283-3294 Department of Biological Sciences 106 Central St. Wellesley MA 02481 USA sbiller@wellesley.edu pointOfContact Krista Longnecker Woods Hole Oceanographic Institution 508-289-2824 266 Woods Hole Road MS# 04 Woods Hole MA 02543 USA klongnecker@whoi.edu pointOfContact Ashley Stein Wellesley College ashleystein06@gmail.com pointOfContact asNeeded Dataset Version: 1 Unknown Biosample_ID SRA_Experiment_ID GEO_Sample_ID Bacterium Carbon_Substrate Timepoint Replicate Illumina NovaSeq X Incubator theme None, User defined NCBI BioSample accession NCBI SRA experiment accession (SRX) accession number seq_descrip treatment time_point replicate featureType BCO-DMO Standard Parameters Automated DNA Sequencer Incubator 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. Collaborative Research: Quantifying the role of microbial extracellular vesicles in marine dissolved organic matter production and consumption https://osprey.bco-dmo.org/project/853399 Collaborative Research: Quantifying the role of microbial extracellular vesicles in marine dissolved organic matter production and consumption <p><em>NSF Award Abstract:</em><br /> Microbial production and consumption of organic carbon play critical roles in the marine food web and global carbon cycling. Bacteria release organic matter in a variety of chemical forms and in diverse contexts, ranging from individual molecules to small aggregates and larger biological particles. In recent years we have come to understand that most, if not all, marine microbes release nanoscale structures called extracellular vesicles from their surfaces. These discrete particles, which are abundant in the oceans, are capable of transporting multiple classes of organic molecules between organisms and can serve as a potential nutrient source for other microbes. Extracellular vesicles thus represent a potentially important component of marine microbial food webs, but the magnitude and dynamics of this contribution are unknown. Further, the packaging of material within vesicles may influence the accessibility of this organic material as compared with truly ‘dissolved’ substances to different groups of marine organisms, potentially biasing nutrient exchanges. Broader impacts of this work is providing hands-on research experiences for female undergraduate students - including those from groups historically underrepresented in STEM fields - and training in data analysis tools.</p> <p>The goal of this project is to advance the understanding of the role that extracellular vesicles play in marine dissolved organic carbon pools and microbial food webs. To determine the contribution of vesicles to organic matter release by marine microbes, the investigators are quantifying the fraction of excreted carbon and nitrogen associated with vesicles released by multiple marine cyanobacteria and heterotrophs. The project is examining how vesicles are ‘consumed’ by heterotrophs to calculate a mass balance of vesicle utilization and produce detailed gene expression data to explore how cells respond to the presence of vesicles. Finally, experiments with coastal and oligotrophic marine communities are providing insights into which organisms utilize vesicles in the field, and whether they are broadly accessible to all microbes or are instead preferentially consumed by a subset of microbes. Collectively, these experiments are opening up a new area of research into the mechanisms underlying the microbial loop and provide foundational insights into the roles of extracellular vesicles in ocean ecosystems.</p> <p>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.</p> VesicleDOM largerWorkCitation project eng; USA biota oceans 2024-08-01 2024-08-31 Laboratory; Vineyard Sound, MA, USA; Bermuda Atlantic Time Series Station 0 BCO-DMO catalogue of parameters from NCBI accession metadata for transcriptomic expression sequences run from cultures of Alteromonas macleodii MIT1002 grown with bacterial extracellular vesicles as a carbon source 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/997668.rdf Name: Biosample_ID Units: unitless Description: <p>NCBI BioSample accession number, contains descriptive information about the physical biological materials</p> http://lod.bco-dmo.org/id/dataset-parameter/997669.rdf Name: SRA_Experiment_ID Units: unitless Description: <p>NCBI Sequence Read Archive accession number for this experimental sample</p> http://lod.bco-dmo.org/id/dataset-parameter/997670.rdf Name: GEO_Sample_ID Units: unitless Description: <p>NCBI Gene Expression Omnibus accession number</p> http://lod.bco-dmo.org/id/dataset-parameter/997671.rdf Name: Bacterium Units: unitless Description: <p>Bacterial strain sequenced</p> http://lod.bco-dmo.org/id/dataset-parameter/997672.rdf Name: Carbon_Substrate Units: unitless Description: <p>Carbon source added to culture</p> http://lod.bco-dmo.org/id/dataset-parameter/997673.rdf Name: Timepoint Units: unitless Description: <p>Culture growth phase when sampled</p> http://lod.bco-dmo.org/id/dataset-parameter/997674.rdf Name: Replicate Units: unitless Description: <p>Biological replicate</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 https://osprey.bco-dmo.org/dataset/997637/data/download download onLine dataset &lt;p&gt;This lab experiment was conducted at Wellesley College, Welleslsey MA in August 2024. &lt;em&gt;Alteromonas macleodii &lt;/em&gt;MIT1002 were grown at 24 °C in a natural seawater-based media containing 0.2 µM filtered, autoclaved seawater supplemented with 3 mM NH&lt;sub&gt;4&lt;/sub&gt;Cl, 50 µM NaH&lt;sub&gt;2&lt;/sub&gt;PO&lt;sub&gt;4&lt;/sub&gt;, Pro99 trace metals, and 0.01% (w/v) glucose. Overnight cultures of &lt;em&gt;Alteromonas&lt;/em&gt; were washed twice in media lacking added glucose (-C). Cultures were diluted to 5e6 cells/mL and supplemented with with either 1x PBS (negative control), &lt;em&gt;Prochlorococcus&lt;/em&gt; extracellular vesicles, &lt;em&gt;Alteromonas&lt;/em&gt; extracellular vesicles, or glucose as a carbon source, each in triplicate. Cultures were incubated at 24°C with shaking at 120 rpm.&amp;nbsp;Samples were collected at two timepoints (representing early and late exponential growth phase) by pelleting at 10,000 xg for 15 minutes, flash freezing on dry ice, and storing at -80 °C. Cells were resuspended and lysed in 600 µL Zymo TriReagent and RNA was extracted using the Zymo Trizol RNA Extraction RNA spin column kit following the manufacturer’s protocol. The columns were washed and treated with DNAse per manufacturers recommendation. RNA was eluted in 50 µL of RNase-free water and quantified using the Qubit RNA High Sensitivity kit (Invitrogen). Ribosomal RNA was depleted using the Qiagen QIAseq FastSelect kit, then the Kapa RNA Hyperprep kit. Paired-end 150nt sequencing data was generated on an Illumina NovaSeq X. RNA library preparation and sequencing was carried out by the &amp;nbsp;Bauer Core Facility (Harvard University).&lt;/p&gt; Specified by the Principal Investigator(s) - Loaded &quot;Alteromonas_GEO_accessions.tsv&quot; (TSV format) using filename as resource name, with &quot;nd&quot; and empty strings treated as missing values - Deleted field &quot;GEO_link&quot; - Reordered fields to: Biosample_ID, SRA_Experiment_ID, GEO_Sample_ID, Bacterium, Carbon_Substrate, Timepoint, Replicate - Renamed resource to &quot;997637_v1_alteromonas_geo_accessions&quot; - Output saved as 997637_v1_alteromonas_geo_accessions.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 NovaSeq X Illumina NovaSeq X PI Supplied Instrument Name: Illumina NovaSeq X PI Supplied Instrument Description:Ribosomal RNA was depleted using the Qiagen QIAseq FastSelect kit, then the Kapa RNA Hyperprep kit. Paired-end 150nt sequencing data was generated on an Illumina NovaSeq X. 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. Incubator Incubator PI Supplied Instrument Name: Incubator PI Supplied Instrument Description:Cultures were incubated at 24°C with shaking at 120 rpm.  Instrument Name: Incubator Instrument Short Name:incubator (general) Instrument Description: A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled. Note: we have more specific terms for shipboard incubators (https://www.bco-dmo.org/instrument/629001) and in-situ incubators (https://www.bco-dmo.org/instrument/494).