http://lod.bco-dmo.org/id/dataset/817298
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
2020-06-30
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Coral gene expression Sequence Read Archive (SRA) accession numbers and information for samples collected at the Flower Garden Banks National Marine Sanctuary in the Gulf of Mexico in September and October of 2017 to capture effects of Hurricane Harvey
2020-06-30
publication
2020-06-30
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-07-08
publication
https://doi.org/10.26008/1912/bco-dmo.817298.1
Sarah W. Davies
Boston University
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: Davies, S. (2020) Coral gene expression Sequence Read Archive (SRA) accession numbers and information for samples collected at the Flower Garden Banks National Marine Sanctuary in the Gulf of Mexico in September and October of 2017 to capture effects of Hurricane Harvey. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-06-30 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.817298.1 [access date]
Dataset Description: <p>To capture the immediate effects of storm-driven freshwater runoff on coral and symbiont physiology, we leveraged the heavy rainfall associated with Hurricane Harvey in late August 2017 by sampling FGB coral gene expression at two time points: September 2017, when surface water salinity was reduced (∼34 ppt); and 1 month later when salinity had returned to typical levels (∼36 ppt in October 2017).&nbsp;</p>
<p>This dataset includes Sequence Read Archive (SRA) and BioSample accessions under BioProject PRJNA552981 at The National Center for Biotechnology Information.&nbsp; It also contains sample information and species names for samples collected the east and west banks of the Flower Garden Banks National Marine Sanctuary (FGBNMS) at 80ft.</p>
<p>These data were published in Wright et al. (2019).</p> Methods and Sampling: <p>Location:&nbsp;</p>
<p>East and west banks of the Flower Garden Banks National Marine Sanctuary (FGBNMS) 80ft<br />
<br />
Sampling Events:<br />
Hurricane Harvey FGB October 2017, Hurricane Harvey FGB October 2018.<br />
<br />
Methodology:&nbsp;<br />
<br />
Tagseq libraries were prepared and SE 50bp reads were generated using Illumina Hiseq 2500 platform.&nbsp;<br />
<br />
Coral tissue samples were preserved midday underwater. RNA was isolated and samples were processed for tagseq profiling.&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1800904 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1800904
completed
Sarah W. Davies
Boston University
617-353-8980
Department of Biology 5 Cummington Mall, Room 215
Boston
MA
02215
US
daviessw@bu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_Name
Time
Bank
Buoy
Lat
Lon
Species
Depth
SRA
Accession
Illumina Hiseq 2500 platform
theme
None, User defined
sample identification
Date_Month
site description
latitude
longitude
taxon
depth
accession number
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
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.
RAPID: Collaborative Research: Impact of freshwater runoff from Hurricane Harvey on coral reef benthic organisms and associated microbial communities
https://osprey.bco-dmo.org/project/746814
RAPID: Collaborative Research: Impact of freshwater runoff from Hurricane Harvey on coral reef benthic organisms and associated microbial communities
<p><em>NSF Award Abstract:</em><br />
Coral reefs are ecologically and economically important ecosystems, and are threatened by a variety of global (climate change) and local (overfishing, pollution) stressors. Anthropogenic climate change is increasing the frequency and severity of storms, which can physically damage reef structures and reduce reef health through changes in seawater quality. In August of 2017, Hurricane Harvey caused widespread flooding in southeast Texas when it released more than 50 trillion liters of rain, which then accumulated along the Texas Shelf. This runoff is expected to impact nearby coral reefs in the Flower Garden Banks National Marine Sanctuary (FGBNMS, northwest Gulf of Mexico) via eddies and jets that transport coastal waters offshore. Findings from this project will allow managers to quickly predict whether extreme storm events are likely to induce reef mortality and ecosystem decline due to freshwater accumulation, by tracking of low salinity water masses coupled with microbial community characterization and metrics of coral health. These data are critical to managing coastal ecosystems, including the high coral cover reefs in the FGBNMS, and will help stakeholders (e.g., diving and fishing communities) plan for and minimize disruption to their livelihoods following these storms. Results will be communicated broadly across scientific arenas, in graduate and undergraduate education and training programs, and to the general public through outreach. The investigators have seven 7 square meter 2-D Reef Replicas from 2014 depicting representative FGBNMS reef bottoms, and will construct additional 2-D Reef Replicas from both banks following the arrival of Harvey runoff, allowing the public to directly experience and quantify the effects of Hurricane Harvey on local reefs using quadrats and identification guides. This project will also synergize with NSF REU programs at Boston University and Texas A&M University, providing transformative research experiences for undergraduates. One post-doctoral scholar, four graduate students, a technician and more than 5 undergraduates will be involved in all aspects of the research. All datasets will be made freely available to the public, and will serve as an important set of baselines for future lines of inquiry into the processes by which hurricanes and other extreme storms impact reef health.</p>
<p>Hurricanes and other extreme storm events can decimate coral reefs through wave-driven physical damage. Freshwater runoff from extreme storms is also potentially detrimental to reefs but has received comparatively less attention. This research will provide unprecedented resolution on how hurricanes and other extreme storm events may trigger cascading interactions among water chemistry, declines in metazoan health and shifts in their associated microbial communities, ultimately resulting in coral reef decline. The freshwater runoff initiated by Hurricane Harvey is likely to impact reefs within the FGBNMS, one of the few remaining coral-dominated reefs in the greater Caribbean. The effects of Harvey runoff will be compared to a previously documented storm-driven runoff event that was associated with invertebrate mortality on the same reef system. Sampling seawater chemistry, microbial communities (water column and benthic), and host gene expression and proteomics before, immediately after, and six months after Harvey runoff enters the FGBNMS will allow us to identify commonalities among large-scale freshwater runoff events and track the response of benthic invertebrate health, microbial community diversity, and the trajectory of reef community recovery or decline. The investigators will determine if changes in water chemistry induce pelagic microbial shifts, if microbial communities typically associated with corals and sponges are altered, and whether feedbacks occur between these potential drivers of benthic invertebrate mortality.</p>
Rapid Reefs Harvey
largerWorkCitation
project
eng; USA
oceans
-93.62828
-93.60019
27.8819
27.908
2017-09-01
2017-10-01
Flower Garden Banks National Marine Sanctuary, Northwest Gulf of Mexico
0
BCO-DMO catalogue of parameters from Coral gene expression Sequence Read Archive (SRA) accession numbers and information for samples collected at the Flower Garden Banks National Marine Sanctuary in the Gulf of Mexico in September and October of 2017 to capture effects of Hurricane Harvey
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/817838.rdf
Name: Sample_Name
Units: unitless
Description: <p>Sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/817839.rdf
Name: Time
Units: unitless
Description: <p>Sample time in format (Full month name and four digit year)</p>
http://lod.bco-dmo.org/id/dataset-parameter/817840.rdf
Name: Bank
Units: unitless
Description: <p>east or west bank of the Flower Garden Banks</p>
http://lod.bco-dmo.org/id/dataset-parameter/817841.rdf
Name: Buoy
Units: unitless
Description: <p>Buoy number samples were collected from</p>
http://lod.bco-dmo.org/id/dataset-parameter/817842.rdf
Name: Lat
Units: decimal degrees
Description: <p>Sample latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/817843.rdf
Name: Lon
Units: decimal degrees
Description: <p>Sample longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/817844.rdf
Name: Species
Units: unitless
Description: <p>Scientific name (Genus species)</p>
http://lod.bco-dmo.org/id/dataset-parameter/817845.rdf
Name: Depth
Units: meters (m)
Description: <p>Sample depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/817846.rdf
Name: SRA
Units: unitless
Description: <p>Sequence Read Archive (SRA) accession number at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/817847.rdf
Name: Accession
Units: unitless
Description: <p>BioSample accession number at NCBI</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
4611
https://darchive.mblwhoilibrary.org/bitstream/1912/25943/1/dataset-817298_hurricane-harvey-coral-gene-expression__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.817298.1
download
onLine
dataset
<p>Location:&nbsp;</p>
<p>East and west banks of the Flower Garden Banks National Marine Sanctuary (FGBNMS) 80ft<br />
<br />
Sampling Events:<br />
Hurricane Harvey FGB October 2017, Hurricane Harvey FGB October 2018.<br />
<br />
Methodology:&nbsp;<br />
<br />
Tagseq libraries were prepared and SE 50bp reads were generated using Illumina Hiseq 2500 platform.&nbsp;<br />
<br />
Coral tissue samples were preserved midday underwater. RNA was isolated and samples were processed for tagseq profiling.&nbsp;</p>
Specified by the Principal Investigator(s)
<p>Coral tissue samples were preserved midday underwater. RNA was isolated and samples were processed for tagseq profiling.&nbsp;<br />
<br />
BCO-DMO Data Manager Processing Notes:<br />
* Originally submitted Excel file Wright_etal_metadada.xlsx extracted to csv file.<br />
* added a conventional header with dataset name, PI name, version date<br />
* modified parameter names to conform with BCO-DMO naming conventions (spaces, +, and - changed to underscores).&nbsp; Units in parentheses removed and added to Parameter Description metadata section.<br />
* blank values (originally submitted as NR)&nbsp;in this dataset are displayed as "nd" for "no data."&nbsp; nd is the default missing data identifier in the BCO-DMO system.<br />
* Combined "Lat Lon" column (e.g. "27°52'54.84", 93°37'41.84") separated into separate lat and lon columns in decimal degree format.</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 Hiseq 2500 platform
Illumina Hiseq 2500 platform
PI Supplied Instrument Name: Illumina Hiseq 2500 platform 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.