http://lod.bco-dmo.org/id/dataset/4007
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
2013-07-30
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Gene expression profiles from high through put Illumina sequencing of multiple long-term evolved lines of Trichodesmium, 2011-2013 (Trichodesmium in High CO2 project)
2013-07-30
publication
2013-07-30
revision
BCO-DMO Linked Data URI
2013-07-30
creation
http://lod.bco-dmo.org/id/dataset/4007
David A. Hutchins
University of Southern California
principalInvestigator
Feixue Fu
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., Fu, F. (2013) Gene expression profiles from high through put Illumina sequencing of multiple long-term evolved lines of Trichodesmium, 2011-2013 (Trichodesmium in High CO2 project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2013-07-30 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/4007 [access date]
gene expression profiles obtained from high through put illumina sequencing of multiple long-term evolved lines of Trichodesmium. Dataset Description: <p>NOTE: This dataset were released at NCBI on 2014-07-11.&nbsp; For questions, please contact Eric Webb, eawebb@usc.edu.</p>
<p>This EAGER funded dataset contains GenBank accession numbers for the gene expression profiles obtained from high through put illumina sequencing of multiple long-term evolved lines of Trichodesmium.&nbsp; In these experiments transcriptome samples (labeled 750) were obtained from cultures grown in either projected year 2100 CO2 levels (~750ppm) or current 380ppm levels (labeled 380) for four years.&nbsp; Additional files include the transcriptomic profiles from cells lines that were switched form their longterm conditions to either lower or higher CO2 conditions.&nbsp; These samples are labeled 750-380 for the switch from high CO2 to low and 380-750 for the switch from low to high.</p> Methods and Sampling:
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1143760 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1143760
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
Feixue Fu
University of Southern California
2137403188
Department of Biology, MC 0371, University of Southern California 3616 Trousdale Pkwy
Los Angeles
CA
90089
USA
ffu@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
accession_number
taxon_code
organism
isolate
BioProject_id
theme
None, User defined
accession number
sample identification
taxon
experiment id
featureType
BCO-DMO Standard Parameters
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.
Gene Expression Patterns in High CO2-Adapted Trichodesmium
https://osprey.bco-dmo.org/project/2277
Gene Expression Patterns in High CO2-Adapted Trichodesmium
<p><i>Project Description from NSF Abstract:</i></p>
<p>The potential for biogeochemically-critical marine organisms, such as the N2-fixing cyanobacterium Trichodesmium, to adapt to a rapidly changing environment is a poorly understood but key determinant of future ocean food webs and elemental cycles. Despite an exponential increase in the sophistication of molecular tools available to the ocean science community, no study has yet applied these methods to relevant marine organisms in conjunction with microbial evolution experiments such as those pioneered by R.E. Lenski and colleagues for the model enteric bacterium Escherichia coli.</p>
<p>Intellectual Merit:<br />
In this EAGER project, the PIs will conduct an exploratory approach that uses tiled microarray methods to evaluate changes in the expression of both coding and non-coding regions of the genome in Trichodesmium cultures that have been maintained in long-term (>3 years) high CO2 adaptation experiments. The objective of this work is to demonstrate that a novel combination of evolutionary experimental techniques and state-of-the-art gene expression methods can be used to yield unique insights into adaptive changes in keystone marine micro-organisms such as Trichodesmium in response to selection by environmental change variables. The over-arching goal is to increase our mechanistic understanding of the ways that evolution could shape the responses of marine biota to future changes in ocean chemistry and climate.</p>
<p>Broader Impacts:<br />
This project will help support and train a new USC Ph.D. student, and research activities will include USC undergraduate biology majors. Public education and communication efforts for this project will be greatly enhanced by an annual series of public outreach and professional colloquia sponsored by a USC-funded "2020" initiative to integrate scientific and societal responses to climate change in the Southern California region. Any evolution-driven shifts in the growth and N2 fixation patterns of Trichodesmium, a keystone oceanic functional group, have large consequences for marine ecology, carbon cycling, and the food chains that support important living resources. The biggest scientific impact of this EAGER project could be to offer verification of a pioneering new approach to help determine how the microbes that are fundamental to today's ocean biogeochemical cycles will adapt to anticipated and unprecedented rates of change in marine ecosystems. </p>
Trichodesmium in High CO2
largerWorkCitation
project
eng; USA
oceans
Southern California
2013-07-30
0
BCO-DMO catalogue of parameters from Gene expression profiles from high through put Illumina sequencing of multiple long-term evolved lines of Trichodesmium, 2011-2013 (Trichodesmium in High CO2 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/35827.rdf
Name: accession_number
Units: unitless
Description: <p>database identifier assigned by repository and linked to GenBank</p>
http://lod.bco-dmo.org/id/dataset-parameter/35828.rdf
Name: taxon_code
Units: unitless
Description: <p>identification number of experimental organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/35829.rdf
Name: organism
Units: unitless
Description: <p>taxonomic name of experimental organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/35830.rdf
Name: isolate
Units: unitless
Description: <p>isolate number of experimental organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/35831.rdf
Name: BioProject_id
Units: unitless
Description: <p>identification code of BioProject experiment</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
1857
https://datadocs.bco-dmo.org/file/QAAXxDOs3npNDJ/trich_accession.csv
trich_accession.csv
Primary data file for dataset ID 4007
download
https://osprey.bco-dmo.org/dataset/4007/data/download
download
onLine
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
Deployment: lab_Webb_Hutchins_Fu
lab_Webb_Hutchins_Fu
Webb-Hutchins-Fu USC
laboratory
Webb-Hutchins-Fu USC
laboratory