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Title Sum-
Institution Dataset ID
     data   graph     files  public 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
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The Dataset's Variables and Attributes

Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson
attribute NC_GLOBAL acquisition_description String Location:\u00a0

East and west banks of the Flower Garden Banks National Marine Sanctuary
(FGBNMS) 80ft

Sampling Events:
Hurricane Harvey FGB October 2017, Hurricane Harvey FGB October 2018.


Tagseq libraries were prepared and SE 50bp reads were generated using Illumina
Hiseq 2500 platform.\u00a0

Coral tissue samples were preserved midday underwater. RNA was isolated and
samples were processed for tagseq profiling.\u00a0
attribute NC_GLOBAL awards_0_award_nid String 746827
attribute NC_GLOBAL awards_0_award_number String OCE-1800904
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1800904 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String Daniel Thornhill
attribute NC_GLOBAL awards_0_program_manager_nid String 722161
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Hurricane Harvey sra samples
PI: Sarah Davies
Data Version 1: 2020-06-30
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3 19 Dec 2019
attribute NC_GLOBAL dataset_current_state String Final and no updates
attribute NC_GLOBAL date_created String 2020-06-30T18:56:47Z
attribute NC_GLOBAL date_modified String 2020-07-08T14:50:47Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.26008/1912/bco-dmo.817298.1
attribute NC_GLOBAL Easternmost_Easting double -93.60019
attribute NC_GLOBAL geospatial_lat_max double 27.908
attribute NC_GLOBAL geospatial_lat_min double 27.8752
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double -93.60019
attribute NC_GLOBAL geospatial_lon_min double -93.81469
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL geospatial_vertical_max double 24.1
attribute NC_GLOBAL geospatial_vertical_min double 19.2
attribute NC_GLOBAL geospatial_vertical_positive String down
attribute NC_GLOBAL geospatial_vertical_units String m
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/817298 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Automated Sequencer
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 817435
attribute NC_GLOBAL instruments_0_description String General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.
attribute NC_GLOBAL instruments_0_instrument_name String Automated DNA Sequencer
attribute NC_GLOBAL instruments_0_instrument_nid String 649
attribute NC_GLOBAL instruments_0_supplied_name String Illumina Hiseq 2500 platform
attribute NC_GLOBAL keywords String accession, bank, bco, bco-dmo, biological, buoy, chemical, data, dataset, depth, dmo, erddap, latitude, longitude, management, name, oceanography, office, preliminary, sample, Sample_Name, species, sra, time, time2
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/817298/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/817298 (external link)
attribute NC_GLOBAL Northernmost_Northing double 27.908
attribute NC_GLOBAL param_mapping String {'817298': {'Lat': 'master - latitude', 'Depth': 'master - depth', 'Lon': 'master - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/817298/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Boston University
attribute NC_GLOBAL people_0_affiliation_acronym String BU
attribute NC_GLOBAL people_0_person_name String Sarah W. Davies
attribute NC_GLOBAL people_0_person_nid String 746829
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String Boston University
attribute NC_GLOBAL people_1_affiliation_acronym String BU
attribute NC_GLOBAL people_1_person_name String Rachel Wright
attribute NC_GLOBAL people_1_person_nid String 817433
attribute NC_GLOBAL people_1_role String Contact
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL people_2_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_2_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_2_person_name String Amber D. York
attribute NC_GLOBAL people_2_person_nid String 643627
attribute NC_GLOBAL people_2_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_2_role_type String related
attribute NC_GLOBAL project String Rapid Reefs Harvey
attribute NC_GLOBAL projects_0_acronym String Rapid Reefs Harvey
attribute NC_GLOBAL projects_0_description String NSF Award Abstract:
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.
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.
attribute NC_GLOBAL projects_0_end_date String 2019-11
attribute NC_GLOBAL projects_0_geolocation String Flower Garden Banks National Marine Sanctuary, Northwest Gulf of Mexico
attribute NC_GLOBAL projects_0_name String RAPID: Collaborative Research: Impact of freshwater runoff from Hurricane Harvey on coral reef benthic organisms and associated microbial communities
attribute NC_GLOBAL projects_0_project_nid String 746814
attribute NC_GLOBAL projects_0_start_date String 2017-12
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL Southernmost_Northing double 27.8752
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL summary String 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 (\u223c34 ppt); and 1 month later when salinity had returned to typical levels (\u223c36 ppt in October 2017). \r\n\r\nThis dataset includes Sequence Read Archive (SRA) and BioSample accessions under BioProject PRJNA552981 at The National Center for Biotechnology Information. 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.\r\n\r\nThese data were published in Wright et al. (2019).
attribute NC_GLOBAL title String 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
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double -93.81469
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.5
variable Sample_Name   String  
attribute Sample_Name bcodmo_name String sample
attribute Sample_Name description String Sample name
attribute Sample_Name long_name String Sample Name
attribute Sample_Name nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute Sample_Name units String unitless
variable time2   String  
attribute time2 bcodmo_name String Date_Month
attribute time2 description String Sample time in format (Full month name and four digit year)
attribute time2 long_name String Time
attribute time2 units String unitless
variable Bank   String  
attribute Bank bcodmo_name String site_descrip
attribute Bank description String east or west bank of the Flower Garden Banks
attribute Bank long_name String Bank
attribute Bank units String unitless
variable Buoy   float  
attribute Buoy _FillValue float NaN
attribute Buoy actual_range float 1.0, 4.0
attribute Buoy bcodmo_name String site_descrip
attribute Buoy description String Buoy number samples were collected from
attribute Buoy long_name String Buoy
attribute Buoy units String unitless
variable latitude   double  
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 27.8752, 27.908
attribute latitude axis String Y
attribute latitude bcodmo_name String latitude
attribute latitude colorBarMaximum double 90.0
attribute latitude colorBarMinimum double -90.0
attribute latitude description String Sample latitude
attribute latitude ioos_category String Location
attribute latitude long_name String Latitude
attribute latitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LATX/ (external link)
attribute latitude standard_name String latitude
attribute latitude units String degrees_north
variable longitude   double  
attribute longitude _CoordinateAxisType String Lon
attribute longitude _FillValue double NaN
attribute longitude actual_range double -93.81469, -93.60019
attribute longitude axis String X
attribute longitude bcodmo_name String longitude
attribute longitude colorBarMaximum double 180.0
attribute longitude colorBarMinimum double -180.0
attribute longitude description String Sample longitude
attribute longitude ioos_category String Location
attribute longitude long_name String Longitude
attribute longitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LONX/ (external link)
attribute longitude standard_name String longitude
attribute longitude units String degrees_east
variable Species   String  
attribute Species bcodmo_name String taxon
attribute Species description String Scientific name (Genus species)
attribute Species long_name String Species
attribute Species units String unitless
variable depth   double  
attribute depth _CoordinateAxisType String Height
attribute depth _CoordinateZisPositive String down
attribute depth _FillValue double NaN
attribute depth actual_range double 19.2, 24.1
attribute depth axis String Z
attribute depth bcodmo_name String depth
attribute depth colorBarMaximum double 8000.0
attribute depth colorBarMinimum double -8000.0
attribute depth colorBarPalette String TopographyDepth
attribute depth description String Sample depth
attribute depth ioos_category String Location
attribute depth long_name String Depth
attribute depth nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/DEPH/ (external link)
attribute depth positive String down
attribute depth standard_name String depth
attribute depth units String m
variable SRA   String  
attribute SRA bcodmo_name String accession number
attribute SRA description String Sequence Read Archive (SRA) accession number at NCBI
attribute SRA long_name String SRA
attribute SRA units String unitless
variable Accession   String  
attribute Accession bcodmo_name String accession number
attribute Accession description String BioSample accession number at NCBI
attribute Accession long_name String Accession
attribute Accession units String unitless

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.

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