http://lod.bco-dmo.org/id/dataset/636756
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
2016-01-28
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Raw LC-MS/MS data, with list of identified peptides, and DNA sequences from a proteomic profile of Mariprofundus ferrooxydans
2016-01-28
publication
2016-01-28
revision
BCO-DMO Linked Data URI
2016-01-28
creation
http://lod.bco-dmo.org/id/dataset/636756
Roman A. Barco
Bigelow Laboratory for Ocean Sciences
principalInvestigator
Katrina Edwards
University of Southern California
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: Barco, R. A., Edwards, K. (2016) Raw LC-MS/MS data, with list of identified peptides, and DNA sequences from a proteomic profile of Mariprofundus ferrooxydans. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 28 Jan 2016) Version Date 2016-01-28 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/636756 [access date]
Raw LC-MS/MS data, with list of identified peptides, and DNA sequences. Dataset Description: <p>Raw LC-MS/MS data, with list of identified peptides in xml format, and&nbsp;DNA sequences.</p>
<p>Related publications:<br />
Barco, RA, Emerson, D, Sylvan, JB, Orcutt, BN, Jacobson Meyers, ME, Ramírez, GA, Zhong, JD, Edwards, KJ. 2015. New insights into microbial iron oxidation as revealed by the proteomic profile of an obligately iron-oxidizing chemolithoautotroph. <em>Appl. Environ. Microbiol.</em> 81(17): 5927-37. doi: <a href="http://dx.doi.org/10.1128/AEM.01374-15" target="_blank">10.1128/AEM.01374-15</a>&nbsp;</p> Methods and Sampling: <p>A proteomic profile of the chemolithoautotrophic, neutrophilic, iron-oxidizing Mariprofundus ferrooxydans was obtained in duplicates and analyzed via LC-MS/MS. Additionally, a proteomic analysis of the membrane fraction is included. Cultures were harvested at late log phase by following the protocol in Barco and Edwards (2014). Briefly, proteins were extracted with 0.1N NaOH/2% SDS solution, clarified and concentrated by nanofiltration. The concentrated samples were run on SDS-PAGE gels in duplicate lanes. All the bands from each lane were excised and analyzed via LC-MS/MS. Membrane fractions were obtained in the following way: the cell-separation protocol was performed per Barco and Edwards (2014) and the cell pellet was resuspended in 0.5M NaCl/40mM Tri-base buffer at pH 8.5 and sonicated for 10 cycles of 30 secs pulses followed by 30 secs of cooling. This sample was clarified and the supernatant was ultracentrifuged at 100,000 x g for 2 hrs. The reddish pellet was solubilized with 0.5% Ultrol Grade, n-Dodecyl-beta-D-maltoside and run on a SDS-PAGE gel. DNA: DNA was extracted by using the FastDNA Spin soil kit according to the manufacturer’s instructions (MP Biomedicals). Extracted DNAwas stored at&nbsp;20 degrees&nbsp;C until processing. Genomic gaps were amplified by PCR on a Veriti thermal cycler (Life Technologies) as follows: 1 step of denaturation at 95 degrees&nbsp;C for 4 min; 35 cycles of denaturation, melting, and extension (95 degrees&nbsp;C for 30 s, 51 degrees&nbsp;C for 30 s, and 72 degrees&nbsp;C for 3 min, respectively); 1 step of extension at 72 degrees&nbsp;C for 10 min; and 1 final step of cooling at 4 degrees&nbsp;C. Primers used for the gap containing the Cyc1PV-1 gene were 79F (5'-GAAGCGATGGGAAATGTGAAT-3') and 375F (5'-CACACTGGAAGATGTTCTGG-3'). Primers used for the gap containing the Cyc2PV-1 gene were 555F (5'-ACTGATGGGTATCAACAACC-3') and 92R (5'-CCTATCTGTACCGAGCATTC-3'). The amplicons were purified by using the QIAquick PCR purification kit (Qiagen). Amplicon sizes were checked in a 1% agarose gel via electrophoresis. Purified PCR amplicons were submitted for Sanger sequencing and primer walking (Laragen).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0939564 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0939564
completed
Roman A. Barco
Bigelow Laboratory for Ocean Sciences
207-315-2567
60 Bigelow Dr.
East Boothbay
ME
04544
USA
rbarco@bigelow.org
pointOfContact
Katrina Edwards
University of Southern California
pointOfContact
asNeeded
Dataset Version: 28 Jan 2016
Unknown
type
taxon
repository
identifier
URL
description
Thermo LTQ-Orbitrap XL
theme
None, User defined
sample type
taxon
external_link
accession number
brief description
featureType
BCO-DMO Standard Parameters
Mass Spectrometer
Thermal Cycler
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 Dark Energy Biosphere Investigations
http://www.darkenergybiosphere.org
Center for Dark Energy Biosphere Investigations
The mission of the Center for Dark Energy Biosphere Investigations (C-DEBI) is to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.
C-DEBI provides a framework for a large, multi-disciplinary group of scientists to pursue fundamental questions about life deep in the sub-surface environment of Earth. The fundamental science questions of C-DEBI involve exploration and discovery, uncovering the processes that constrain the sub-surface biosphere below the oceans, and implications to the Earth system. What type of life exists in this deep biosphere, how much, and how is it distributed and dispersed? What are the physical-chemical conditions that promote or limit life? What are the important oxidation-reduction processes and are they unique or important to humankind? How does this biosphere influence global energy and material cycles, particularly the carbon cycle? Finally, can we discern how such life evolved in geological settings beneath the ocean floor, and how this might relate to ideas about the origin of life on our planet?
C-DEBI's scientific goals are pursued with a combination of approaches:
(1) coordinate, integrate, support, and extend the research associated with four major programs—Juan de Fuca Ridge flank (JdF), South Pacific Gyre (SPG), North Pond (NP), and Dorado Outcrop (DO)—and other field sites;
(2) make substantial investments of resources to support field, laboratory, analytical, and modeling studies of the deep subseafloor ecosystems;
(3) facilitate and encourage synthesis and thematic understanding of submarine microbiological processes, through funding of scientific and technical activities, coordination and hosting of meetings and workshops, and support of (mostly junior) researchers and graduate students; and
(4) entrain, educate, inspire, and mentor an interdisciplinary community of researchers and educators, with an emphasis on undergraduate and graduate students and early-career scientists.
Note: Katrina Edwards was a former PI of C-DEBI; James Cowen is a former co-PI.
Data Management:
C-DEBI is committed to ensuring all the data generated are publically available and deposited in a data repository for long-term storage as stated in their Data Management Plan (PDF) and in compliance with the NSF Ocean Sciences Sample and Data Policy. The data types and products resulting from C-DEBI-supported research include a wide variety of geophysical, geological, geochemical, and biological information, in addition to education and outreach materials, technical documents, and samples. All data and information generated by C-DEBI-supported research projects are required to be made publically available either following publication of research results or within two (2) years of data generation.
To ensure preservation and dissemination of the diverse data-types generated, C-DEBI researchers are working with BCO-DMO Data Managers make data publicly available online. The partnership with BCO-DMO helps ensure that the C-DEBI data are discoverable and available for reuse. Some C-DEBI data is better served by specialized repositories (NCBI's GenBank for sequence data, for example) and, in those cases, BCO-DMO provides dataset documentation (metadata) that includes links to those external repositories.
C-DEBI
largerWorkCitation
program
Proteomic profiling of neutrophilic, iron-oxidizing Mariprofundus ferrooxydans, strain PV-1
https://osprey.bco-dmo.org/project/632643
Proteomic profiling of neutrophilic, iron-oxidizing Mariprofundus ferrooxydans, strain PV-1
<p>Description from <a href="http://www.darkenergybiosphere.org/education/graduatesFunded.html" target="_blank">C-DEBI website</a>:<br />
The aim of this proposal is to gain a better understanding of what subsets of proteins are actually being expressed during neutrophilic, microbial iron (Fe)-oxidation. The recently isolated <em>Mariprofundus ferrooxydans</em>, strain PV-1, will be used as a marine model organism to investigate proteomic differences under different Fe substrates: aqueous Fe2+ and solid Fe0. Two-dimensional gel electrophoresis (2D-GE) and shotgun proteomic methods (LC-MS/MS) will be employed to obtain results from the cultures grown under different conditions. The research being proposed would constitute the foundation for the development of diagnostic tools for the accordance, distribution, and activity level of Fe-oxidation, a globally important biogeochemical process at and below the ocean floor.</p>
<p>This project was funded by a C-DEBI Graduate Student Fellowship.</p>
Proteomic profiling of Mariprofundus ferrooxydans
largerWorkCitation
project
eng; USA
biota
oceans
2016-01-28
0
BCO-DMO catalogue of parameters from Raw LC-MS/MS data, with list of identified peptides, and DNA sequences from a proteomic profile of Mariprofundus ferrooxydans
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/636764.rdf
Name: type
Units: dimensionless
Description: <p>Description of sample type.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636765.rdf
Name: taxon
Units: dimensionless
Description: <p>Taxon studied.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636766.rdf
Name: repository
Units: dimensionless
Description: <p>Name of the repository where the raw data are stored.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636767.rdf
Name: identifier
Units: dimensionless
Description: <p>Unique identifer: Either the PRIDE database project identifier or the NCBI accession number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636768.rdf
Name: URL
Units: dimensionless
Description: <p>Link to the PRIDE database or NCBI.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636769.rdf
Name: description
Units: dimensionless
Description: <p>Description of the method and sample.</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
1999
https://datadocs.bco-dmo.org/file/933jzx6H2WYyjL/raw_LCMS_DNA.csv
raw_LCMS_DNA.csv
Primary data file for dataset ID 636756
download
https://osprey.bco-dmo.org/dataset/636756/data/download
download
onLine
dataset
<p>A proteomic profile of the chemolithoautotrophic, neutrophilic, iron-oxidizing Mariprofundus ferrooxydans was obtained in duplicates and analyzed via LC-MS/MS. Additionally, a proteomic analysis of the membrane fraction is included. Cultures were harvested at late log phase by following the protocol in Barco and Edwards (2014). Briefly, proteins were extracted with 0.1N NaOH/2% SDS solution, clarified and concentrated by nanofiltration. The concentrated samples were run on SDS-PAGE gels in duplicate lanes. All the bands from each lane were excised and analyzed via LC-MS/MS. Membrane fractions were obtained in the following way: the cell-separation protocol was performed per Barco and Edwards (2014) and the cell pellet was resuspended in 0.5M NaCl/40mM Tri-base buffer at pH 8.5 and sonicated for 10 cycles of 30 secs pulses followed by 30 secs of cooling. This sample was clarified and the supernatant was ultracentrifuged at 100,000 x g for 2 hrs. The reddish pellet was solubilized with 0.5% Ultrol Grade, n-Dodecyl-beta-D-maltoside and run on a SDS-PAGE gel. DNA: DNA was extracted by using the FastDNA Spin soil kit according to the manufacturer’s instructions (MP Biomedicals). Extracted DNAwas stored at&nbsp;20 degrees&nbsp;C until processing. Genomic gaps were amplified by PCR on a Veriti thermal cycler (Life Technologies) as follows: 1 step of denaturation at 95 degrees&nbsp;C for 4 min; 35 cycles of denaturation, melting, and extension (95 degrees&nbsp;C for 30 s, 51 degrees&nbsp;C for 30 s, and 72 degrees&nbsp;C for 3 min, respectively); 1 step of extension at 72 degrees&nbsp;C for 10 min; and 1 final step of cooling at 4 degrees&nbsp;C. Primers used for the gap containing the Cyc1PV-1 gene were 79F (5'-GAAGCGATGGGAAATGTGAAT-3') and 375F (5'-CACACTGGAAGATGTTCTGG-3'). Primers used for the gap containing the Cyc2PV-1 gene were 555F (5'-ACTGATGGGTATCAACAACC-3') and 92R (5'-CCTATCTGTACCGAGCATTC-3'). The amplicons were purified by using the QIAquick PCR purification kit (Qiagen). Amplicon sizes were checked in a 1% agarose gel via electrophoresis. Purified PCR amplicons were submitted for Sanger sequencing and primer walking (Laragen).</p>
Specified by the Principal Investigator(s)
<p>Excised bands were trypsin-digested and submitted for LC-MS/MS analysis which involved a Thermo LTQ-Orbitrap XL mass spectrometer equipped with an Eksigent Nanoliquid Chromatography 1-D plus system. The resulting MS/MS spectra were searched against the proteomes of Mariprofundus ferrooxydans strains PV-1(Uniprot database) and M34 (IMG database) using Proteome Discoverer SEQUEST Daemon search engine. DNA: sequences were analyzed in Geneious v. R6 (Biomatters Ltd.).</p>
<p>Raw LC-MS/MS files are publicly available through the PRIDE Archive at <a href="http://www.ebi.ac.uk/pride/archive/projects/PXD001050">http://www.ebi.ac.uk/pride/archive/projects/PXD001050</a> and <a href="http://www.ebi.ac.uk/pride/archive/projects/PXD001439">http://www.ebi.ac.uk/pride/archive/projects/PXD001439</a>.</p>
<p>DNA sequences were deposited in Genbank under accession numbers KR106296,&nbsp;KR106297,&nbsp;KR091570,&nbsp;and BK009249.</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:Excised bands were trypsin-digested and submitted for LC-MS/MS analysis which involved a Thermo LTQ-Orbitrap XL mass spectrometer equipped with an Eksigent Nanoliquid Chromatography 1-D plus system. 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/
PI Supplied Instrument Name: Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)