http://lod.bco-dmo.org/id/dataset/726901
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
2018-02-14
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
NCBI accessions for raw RNA-seq fastq in 380 and 750 uatm CO2 from experiments conducted at the University of Southern California: deep metatranscriptomic sequencing of Trichodesmium enrichment cultures (HiCO2_AdaptCyano project)
2018-02-14
publication
2018-02-14
revision
BCO-DMO Linked Data URI
2018-02-14
creation
http://lod.bco-dmo.org/id/dataset/726901
David A. Hutchins
University of Southern California
principalInvestigator
Eric A. Webb
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: Hutchins, D. A., Webb, E. A. (2018) NCBI accessions for raw RNA-seq fastq in 380 and 750 uatm CO2 from experiments conducted at the University of Southern California: deep metatranscriptomic sequencing of Trichodesmium enrichment cultures (HiCO2_AdaptCyano project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2018-02-14 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/726901 [access date]
NCBI accession numbers for raw RNA-seq fastq files derived from laboratory-maintained Trichodesmium erythraeum cultures Dataset Description: <p>These data were derived from laboratory-maintained Trichodesmium erythraeum cultures and contain accessions and links to raw RNA-seq fastq files&nbsp;in NCBI’s Gene Expression Omnibus, accessible through GEO Series accession number <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE94951" target="_blank">GSE94951</a>. The sample accession numbers corresponding to the low and high CO2 samples from this work are <a href="https://www.ncbi.nlm.nih.gov/biosample/?term=GSM2492342" target="_blank">GSM2492342</a>, <a href="https://www.ncbi.nlm.nih.gov/biosample/?term=GSM2492343" target="_blank">GSM2492343</a>, <a href="http://www.ncbi.nlm.nih.gov/biosample/?term=GSM2492344" target="_blank">GSM2492344</a>, and <a href="http://www.ncbi.nlm.nih.gov/biosample/?term=GSM2492345" target="_blank">GSM2492345</a>.</p>
<p>These data were reported in the paper (Lee et al., 2017) &nbsp;<br />
<div>&nbsp;</div> Methods and Sampling: <p>Culturing: Cultures of Trichodesmium erythraeum strain IMS101 were maintained at the University of Southern California, Los Angeles, California, USA, in modified Aquil medium with no fixed nitrogen provided. Cultures were grown at 26ºC in a light:dark cycle of 12:12, and maintained under 120 µmol photons per m^2 s^-1.</p>
<p>Samples GSM2492342 and GSM2492343 were grown as noted above, but under 380 µatm CO2.</p>
<p>Samples GSM2492344 and GSM2492345 were grown as noted above, but under 800 µatm CO2.</p>
<p>Sampling: Cultures were filtered onto 5 µm polycarbonate filters during the middle of the photoperiod, flash frozen, and stored in liquid nitrogen until RNA extraction.&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1260233 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1260233
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1657757 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1657757
completed
David A. Hutchins
University of Southern California
213-740-5616
Department of Biological Sciences 3616 Trousdale Parkway, AHF 20
Los Angeles
CA
90089
USA
dahutch@usc.edu
pointOfContact
Eric A. Webb
University of Southern California
213-740-7954
Department of Biological Sciences, Marine and Environmental Biology Section; Dornsife College of Letters, Arts, and Sciences 3616 Trousdale Parkway AHF 331
Los Angeles
CA
90089-0371
USA
eawebb@usc.edu
pointOfContact
asNeeded
Unknown
organism_community
pCO2
BioSample
SRA
GSM
GSM_link
Illumina Hi-Seq
theme
None, User defined
taxon
Partial pressure of CO2
accession number
external_link
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
lab_Webb_Hutchins_Fu
service
Deployment Activity
Southern California
place
Locations
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.
Adaptation of key N2-fixing cyanobacteria to changing CO2
https://osprey.bco-dmo.org/project/551230
Adaptation of key N2-fixing cyanobacteria to changing CO2
<p><em>Description from NSF award abstract:</em><br />
This study will employ a novel combination of experimental evolution techniques and state-of-the-art molecular methods to yield unique insights into adaptive changes in the keystone marine cyanobacteria <em>Trichodesmium</em> and <em>Crocosphaera</em> in response to selection by high CO2. Several studies have suggested that N2-fixation rates of the biogeochemically-critical cyanobacteria <em>Trichodesmium</em> and <em>Crocosphaera</em> may increase dramatically in the future high CO2 ocean, but these have all used the same limited set of cultured isolates and considered cells only briefly acclimated to elevated CO2. The investigator's new results, however, demonstrate that a broad diversity of high- and low-CO2 adapted ecotypes exists within each diazotroph genus. Furthermore, in a preliminary four year experimental evolution study with <em>Trichodesmium</em>, the PIs observed large adaptive responses following 500-700 generations of selection by high CO2- but in a completely unexpected way. All of the six replicate high CO2-adapted cell lines exhibited strong constitutive up-regulation of N2 fixation rates. These very elevated N2 fixation rates continued, even though the cultures have were switched back to low-CO2 conditions for many months. Expression of the nif operon and N assimilatory genes was also up-regulated in these cell lines, as is expression of many intergenic regions of the genome.</p>
<p><strong>The investigators hypothesize that constitutive up-regulation of cellular N2 fixation systems may be a common adaptive response of both <em>Trichodesmium</em> and <em>Crocosphaera</em> under extended selection by elevated CO2. This project will test this hypothesis in a four-year experimental evolution study to determine the adaptive responses of both high- and low-CO2 specialized ecotypes of these two diazotrophs to increased CO2.</strong></p>
<p>The investigators will grow representative high- and low-CO2 adapted ecotypes from each genus in well-replicated cell lines at 380 ppm and 750 ppm CO2 for up to 1000 generations. Periodically, they will perform "switch" experiments to measure N2 and CO2 fixation rates and growth rates of high CO2-selected cell lines grown briefly (one week) at low CO2, and vice versa. These switch experiments will allow screening for cell lines which exhibit adaptive changes in phenotypically-expressed rate parameters, such as those observed in the preliminary <em>Trichodesmium</em> study. Evolutionary mechanisms in the CO2-selected cell lines will be examined by comparison of changes in their genomes, transcriptomes, and proteomes over time relative to reference genomes, using frozen samples archived monthly during the preceding selection period. Examination of these molecular and biochemical changes will be coordinated with an in-depth array of physiological and biogeochemical analyses. This combined approach will allow an evaluation of potential adaptive mechanisms in diazotrophic cyanobacteria ranging from indel, duplication, single nucleotide polymorphism, and transposition mutations to altered putative non-coding RNA expression, protein expression, and post-translational protein modifications, and then allow the investigators to link these mechanisms directly with their potential impacts on ecosystem-level biogeochemical processes like N2 and CO2 fixation. Finally, the research team will determine how long term selection by high CO2 affects the iron and phosphorus requirements of <em>Trichodesmium </em>and <em>Crocosphaera</em>, since constitutive up-regulation of N2 fixation would also have major implications for limitation of diazotrophs by these two critical nutrients in the future high CO2 ocean.</p>
HiCO2_AdaptCyano
largerWorkCitation
project
Collaborative Research: Iron and phosphorus balanced limitation of nitrogen fixation in the oligotrophic ocean
https://osprey.bco-dmo.org/project/724451
Collaborative Research: Iron and phosphorus balanced limitation of nitrogen fixation in the oligotrophic ocean
<p>NSF abstract:</p>
<p>Marine cyanobacteria are able to use or "fix" atmospheric nitrogen gas, and so supply much of the essential nutrient nitrogen that supports open ocean food chains. Oceanographers have usually thought that the growth of these nitrogen-fixing cyanobacteria is limited at any particular time and place by the supply of either iron, or of phosphorus. Preliminary experiments have shown, though, that these nitrogen fixers instead grow best when both iron and phosphorus are scarce at the same time. In this project, the researchers will use cellular indicators that are specific for iron and phosphorus limitation to determine how important this type of "balanced limitation" of nitrogen-fixing cyanobacteria is in controlling the productivity of ocean food chains in the tropical Atlantic Ocean. Two graduate students will be trained at the University of Southern California (USC) and Woods Hole Oceanographic Institution, as well as a postdoctoral researcher at USC. Educational outreach efforts will take place at a Los Angeles inner city high school with a student body that is over 98% Hispanic and African-American, and with underrepresented undergraduates in the USC Global Environmental Microbiology course. In addition, two Research Experiences for Undergraduates students will be supervised for summer research projects to help them learn about science career options.</p>
<p>The researchers will investigate the biological and biogeochemical consequences of this unique balanced iron/phosphorus-limited phenotype, using both laboratory and fieldwork approaches. During the first year of this project, the nitrogen-fixing cyanobacteria will be cultured under iron and/or phosphorus limitation, followed by application of proteomics and transcriptomics to identify genes that are potential diagnostic biomarkers for iron/phosphorus balanced limitation. Preliminary work has already identified one promising candidate biomarker in one cyanobacterium, an EzrA protein domain that appears to be associated with the cell size decreases seen specifically under balanced limitation, and the researchers have identified numerous other potential candidates for similar biomarkers. During the second year, these new co-limitation biomarkers and others previously validated for iron limitation (IsiB) and phosphorus limitation (SphX) will be used to investigate balanced limitation during a research cruise transecting from relatively high-iron, low-phosphorus North Atlantic waters, to the relatively high-phosphorus, low-iron South Atlantic. This fieldwork component will survey nitrogen fixing cyanobacteria populations across this natural iron/phosphorus gradient for genetic, proteomic, and physiological indicators of balanced limitation, as well as testing their responses to iron and phosphorus manipulations in shipboard incubation experiments. The third year will be devoted to sample analysis, and publications exploring the responses of oceanic nitrogen fixers to simultaneous limitation by both iron and phosphorus.</p>
TriCoLim
largerWorkCitation
project
eng; USA
biota
oceans
Southern California
2018-02-14
From projects that focused on the following 2 locations: 1. Culture study at the University of Southern California, Los Angeles 2. Tropical Atlantic
0
BCO-DMO catalogue of parameters from NCBI accessions for raw RNA-seq fastq in 380 and 750 uatm CO2 from experiments conducted at the University of Southern California: deep metatranscriptomic sequencing of Trichodesmium enrichment cultures (HiCO2_AdaptCyano 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/726955.rdf
Name: organism_community
Units: unitless
Description: <p>host organism from which the microbial community genomic material was extracted</p>
http://lod.bco-dmo.org/id/dataset-parameter/726956.rdf
Name: pCO2
Units: microatmospheres
Description: <p>CO2 level of culture</p>
http://lod.bco-dmo.org/id/dataset-parameter/726957.rdf
Name: BioSample
Units: unitless
Description: <p>NCBI BioSample accession number: descriptive information about the physical biological materials</p>
http://lod.bco-dmo.org/id/dataset-parameter/726958.rdf
Name: SRA
Units: unitless
Description: <p>NCBI Sequence Read Archive accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/726959.rdf
Name: GSM
Units: unitless
Description: <p>NCBI sample Gene Expression Omnibus accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/726960.rdf
Name: GSM_link
Units: unitless
Description: <p>link to NCBI BioSample (GSM) accession webpage for the GSM</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
719
https://datadocs.bco-dmo.org/file/JEE1M8BCy490OL/Tricho_FASTq_accessions.csv
Tricho_FASTq_accessions.csv
Primary data file for dataset ID 726901
download
https://osprey.bco-dmo.org/dataset/726901/data/download
download
onLine
dataset
<p>Culturing: Cultures of Trichodesmium erythraeum strain IMS101 were maintained at the University of Southern California, Los Angeles, California, USA, in modified Aquil medium with no fixed nitrogen provided. Cultures were grown at 26ºC in a light:dark cycle of 12:12, and maintained under 120 µmol photons per m^2 s^-1.</p>
<p>Samples GSM2492342 and GSM2492343 were grown as noted above, but under 380 µatm CO2.</p>
<p>Samples GSM2492344 and GSM2492345 were grown as noted above, but under 800 µatm CO2.</p>
<p>Sampling: Cultures were filtered onto 5 µm polycarbonate filters during the middle of the photoperiod, flash frozen, and stored in liquid nitrogen until RNA extraction.&nbsp;</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing Notes:</strong><br />
- created a table with a conventional header with dataset name, PI name, version date<br />
- records were compiled from NCBI website; accessions obtained from&nbsp; (Lee et al., 2017).<br />
- hyperlink were&nbsp;created to the NCBI accessions pages.</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
Illumina Hi-Seq
Illumina Hi-Seq
PI Supplied Instrument Name: Illumina Hi-Seq PI Supplied Instrument Description:Used to sequence the extracted RNA, performed at UC San Diego Institute for Genomic Medicine 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.
Deployment: lab_Webb_Hutchins_Fu
lab_Webb_Hutchins_Fu
Webb-Hutchins-Fu USC
laboratory
Webb-Hutchins-Fu USC
laboratory