http://lod.bco-dmo.org/id/dataset/890877
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
2023-03-01
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Single cell mass spectroscopy data collected to investigate metabolomics affected by cell-cell interactions in 2020 and 2021
2023-03-01
publication
2023-03-01
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-03-07
publication
https://doi.org/10.26008/1912/bco-dmo.890877.1
Zhibo Yang
University of Oklahoma
principalInvestigator
Linda Atkinson
University of Oklahoma
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: Yang, Z., Atkinson, L., Peng, Z. (2023) Single cell mass spectroscopy data collected to investigate metabolomics affected by cell-cell interactions in 2020 and 2021. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-03-01 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.890877.1 [access date]
Methods and Sampling: <p>Cell-cell interaction systems: the device utilized for the indirect co-culture system was Corning Transwell inserts (Corning Incorporated Life Science, Tewsbury, MA, USA) in the format of a 6-well plate with a permeable membrane (pore size: 0.4 µm). Gridded glass coverslips (ibidi USA Incorporation, Fitchburg, WI, USA) were used for cell attachment in the direct co-culture system.</p>
<p>The materials used to fabricate the single-probe include dual-bore quartz tubing (O.D. 500 µm, I.D. 127 µm, Friedrich &amp; Dimmock, Inc., Millville, NJ, USA) and fused silica capillary (O.D. 105 µm, I.D. 40 µm, Polymicro Technologies, Phoenix, AZ, USA). The Single-probe was fabricated following our published protocols. Briefly, three major components (i.e., a Nano-ESI emitter, a dual-bore quartz tip, and a fused silica capillary) were integrated to prepare a Single-probe. Dual-bore quartz needles were produced by pulling the dual-bore quartz tubing using a laser micropipette puller (Sutter P-2000, Sutter Instrument, Novato, CA). The nano-ESI emitters were pulled from the fused silica capillaries using a butane micro torch. A Single-probe was fabricated by embedding a fused silica capillary and a nano-ESI emitter into those two channels of a dual-bore quartz needle. The Single-probe was coupled to a Thermo LTQ Orbitrap XL mass spectrometer for SCMS analysis. The sampling solvent (acetonitrile supplemented with 1% formic acid) was used for the SCMS experiment at a flow rate of ~0.05 µl/min.<br />
<br />
Instruments<br />
The Thermo LTQ Orbitrap XL mass spectrometer (Thermo Scientific, Waltham, MA, United States) was used. The SCMS experiment parameters included a mass range of m/z 200-1500 for positive ion mode and m/z 50-900 for negative ion mode, mass resolution 60,000, ionization voltage 4.5 kV, 1 microscan, and 100 ms max injection time.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1634630 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1634630
completed
Zhibo Yang
University of Oklahoma
405-325-1772
101 Stephenson Parkway Department of Chemistry and Biochemistry
Norman
Oklahoma
73019
USA
zhibo.yang@ou.edu
pointOfContact
Linda Atkinson
University of Oklahoma
405-325-1267
K20-Center 3100 Monitor Ave, Suite 200
Norman
OK
73072
United States
latkinson@ou.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Ion_Mode
Cell_Line
Cell_Number
Description
Mass_to_Charge
Intensity
Relative
path_name
Thermo LTQ Orbitrap XL
theme
None, User defined
sampling_method
sample description
mass-to-charge ratio (m/z)
Intensity (relative ion abundance)
file_name
featureType
BCO-DMO Standard Parameters
Mass Spectrometer
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: Creatine Cycling in Marine Bacterial and Phytoplankton Assemblages
https://osprey.bco-dmo.org/project/709493
Collaborative Research: Creatine Cycling in Marine Bacterial and Phytoplankton Assemblages
<p><em>NSF Award Abstract:</em><br />
High rates of dissolved organic nitrogen (DON) production and utilization in aquatic systems are typically attributed to microbial activity. Though it is known that there is a tight coupling between the production and consumption of biologically available DON, the composition, dynamics, and ecological significance of this rapidly cycled DON pool are less well understood. This proposal focuses on a component of the DON pool, creatine, which is historically understood as a product of metazoan activity, but appears to be both produced by phytoplankton and consumed by marine bacteria. Creatine is present in seawater in measurable quantities, which led to the hypothesis that creatine may be a significant component of the marine DON cycle. DON cycling likely has a bearing on fundamental marine ecosystem processes with large implications for carbon and nitrogen turnover on a global scale. Broader impacts of this project will include outreach that focuses on connecting scientists with K-12 students through research experiences for teachers and lesson development in collaboration with the K20 Center for Educational and Community Renewal, a statewide education research and development center at the University of Oklahoma. The project will integrate the research with inquiry-based teaching of rural secondary science teachers through Authentic Research Experiences in oceanographic science and microbial ecology. The K20 network includes 96% of Oklahoma schools, providing a unique opportunity to impact STEM education in Oklahoma.</p>
<p>The results of this project will help develop a better understanding of DON cycling, the ecological context of creatine uptake activity, and identify both creatine-producing and consuming organisms in the marine environment. The importance of creatine cycling will be assessed via 15N tracer studies along the natural coastal-to-offshore productivity gradient observed in the North Atlantic. Tracer and molecular approaches will be used to investigate the importance of phytoplankton vs. bacteria in creatine uptake and, the taxonomic identities of creatine-utilizing bacteria will be interrogated via molecular, stable isotope probing (SIP), and RT-qPCR approaches.</p>
Creatine Cycling
largerWorkCitation
project
eng; USA
oceans
2020-01-01
2021-01-01
Atlantic bight
0
BCO-DMO catalogue of parameters from Single cell mass spectroscopy data collected to investigate metabolomics affected by cell-cell interactions in 2020 and 2021
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/891033.rdf
Name: Ion_Mode
Units: unitless
Description: <p>Ion mode (pos=positive ion mode, neg=negative ion mode)</p>
http://lod.bco-dmo.org/id/dataset-parameter/891034.rdf
Name: Cell_Line
Units: unitless
Description: <p>The specific cell line that was used for studying cell-cell interactions in co-culture systems.</p>
http://lod.bco-dmo.org/id/dataset-parameter/891035.rdf
Name: Cell_Number
Units: unitless
Description: <p>Cell number for each Cell_Line and Ion mode.</p>
http://lod.bco-dmo.org/id/dataset-parameter/891036.rdf
Name: Description
Units: unitless
Description: <p>Cell with or without co-culture in cell-cell interaction experiments. (e.g. "Control cell line" or "Cell-cell interaction cell line (with resistance)").</p>
http://lod.bco-dmo.org/id/dataset-parameter/891037.rdf
Name: Mass_to_Charge
Units: unitless
Description: <p>Mass to charge ratio (m/z). This is the m/z for ions detected in single cell</p>
http://lod.bco-dmo.org/id/dataset-parameter/891038.rdf
Name: Intensity
Units: unitless
Description: <p>The intensity of ions at m/z</p>
http://lod.bco-dmo.org/id/dataset-parameter/891039.rdf
Name: Relative
Units: unitless
Description: <p>relative intensity normalized by highest peak intensity (100%)</p>
http://lod.bco-dmo.org/id/dataset-parameter/891040.rdf
Name: path_name
Units: unitless
Description: <p>Path name of the same data in an alternate format. This path name is the corresponding csv file containing the same m.z,Intensity, Relative data columns within the file bundle "single_cell_csvs.zip" which contains a csv file per cell. See processing notes section for more information.</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
542838732
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/2eb7618a-1ebe-5cca-a05f-8ed311ccdf49/content
download
https://doi.org/10.26008/1912/bco-dmo.890877.1
download
onLine
dataset
<p>Cell-cell interaction systems: the device utilized for the indirect co-culture system was Corning Transwell inserts (Corning Incorporated Life Science, Tewsbury, MA, USA) in the format of a 6-well plate with a permeable membrane (pore size: 0.4 µm). Gridded glass coverslips (ibidi USA Incorporation, Fitchburg, WI, USA) were used for cell attachment in the direct co-culture system.</p>
<p>The materials used to fabricate the single-probe include dual-bore quartz tubing (O.D. 500 µm, I.D. 127 µm, Friedrich &amp; Dimmock, Inc., Millville, NJ, USA) and fused silica capillary (O.D. 105 µm, I.D. 40 µm, Polymicro Technologies, Phoenix, AZ, USA). The Single-probe was fabricated following our published protocols. Briefly, three major components (i.e., a Nano-ESI emitter, a dual-bore quartz tip, and a fused silica capillary) were integrated to prepare a Single-probe. Dual-bore quartz needles were produced by pulling the dual-bore quartz tubing using a laser micropipette puller (Sutter P-2000, Sutter Instrument, Novato, CA). The nano-ESI emitters were pulled from the fused silica capillaries using a butane micro torch. A Single-probe was fabricated by embedding a fused silica capillary and a nano-ESI emitter into those two channels of a dual-bore quartz needle. The Single-probe was coupled to a Thermo LTQ Orbitrap XL mass spectrometer for SCMS analysis. The sampling solvent (acetonitrile supplemented with 1% formic acid) was used for the SCMS experiment at a flow rate of ~0.05 µl/min.<br />
<br />
Instruments<br />
The Thermo LTQ Orbitrap XL mass spectrometer (Thermo Scientific, Waltham, MA, United States) was used. The SCMS experiment parameters included a mass range of m/z 200-1500 for positive ion mode and m/z 50-900 for negative ion mode, mass resolution 60,000, ionization voltage 4.5 kV, 1 microscan, and 100 ms max injection time.</p>
Specified by the Principal Investigator(s)
<p>Data processing<br />
Single cell data was exported from the mass spec .raw files into Excel Sheets and submitted to BCO-DMO.&nbsp; &nbsp;Each individual table was concatenated into a cohesive table (see BCO-DMO data manager processing notes).<br />
<br />
Metabolites data from single cells were searched against three online metabolomics databases (Metlin, HMDB, and GNPS) for tentative labeling. Tandem MS (MS2) analyses were performed for molecular structure verifications.<br />
<br />
BCO-DMO Data Manager Processing Notes:<br />
* All Sheets from Excel files "Cell-cell interaction project_neg.xlsx" and "Cell-cell interaction project_pos.xlsx" were exported as a csv file per sheet. These sheets were bundled together with a sheet inventory providing experimental metadata to and made available as a supplemental file "single_cell_csvs.zip."&nbsp;<br />
* Each cell table (csv) was imported into the BCO-DMO&nbsp; data system totaling 199 tables.&nbsp; These were concatenated into a cohesive table with additional columns to for metadata contained in the original excel filename,&nbsp; and sheet name.<br />
*&nbsp;Additional Columns "Ion_mode" "Cell_Line" "Cell_Number" and "Description" were added to the combined data table&nbsp;using a lookup table provided by the data submitter&nbsp;that matched information about each Sheet position in the Excel file and which Cell line and cell number it corresponded to.<br />
* sheet inventory and combined data table were reviewed by the original data submitter to&nbsp;ensure the provided metadata was represented accurately in the published data.</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
Thermo LTQ Orbitrap XL
Thermo LTQ Orbitrap XL
PI Supplied Instrument Name: Thermo LTQ Orbitrap XL PI Supplied Instrument Description:Thermo LTQ Orbitrap XL mass spectrometer (Thermo Scientific, Waltham, MA, United States) Instrument Name: Mass Spectrometer Instrument Short Name:Mass Spec Instrument Description: General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/