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   set  data   graph     files  public Coral colony genetic sequence accession numbers for samples collected from the lagoon
environment of Ofu Island, American Samoa between 2011 and 2015.
   ?     I   M   background (external link) RSS BCO-DMO bcodmo_dataset_762497

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 Seven colonies of A. hyacinthus from the back-reef environment of Ofu Island
were tagged, sampled, and monitored at five time-points spanning the bleaching
event: before bleaching representing baseline expression levels (August 2011),
and then two months (April 2015), six months (August 2015), 10 months
(December 2015) and 12 months (February 2016) after initial bleaching was
observed in February 2015. Coral nubbins of approximately 24 cm in size were
collected from colonies within 3 h of high-tide using garden clippers and
preserved in RNAlater. All colonies occurred at depths of approximately 0.51.0
m and were within a 2500 m2area of back-reef. Total RNA was extracted from
tissue samples using Qiagen's RNAeasy Plus Kit, and 35 cDNA libraries (seven
colonies for five dates) were generated using the Illumina TruSeq RNA Library
Prep Kit v2 with Protoscript II Reverse Transcriptase. The 35 libraries were
multiplexed and sequenced across three lanes on a Hiseq2500 at the University
of Utah Microarray and Genomic Analysis Core Facility.

Location: Ofu Island, American Samoa. All data and samples were collected from
the lagoon environment in the National Park of American Samoa at depths less
than 3.0m.
attribute NC_GLOBAL awards_0_award_nid String 647913
attribute NC_GLOBAL awards_0_award_number String OCE-1547921
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1547921 (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 Dr David L. Garrison
attribute NC_GLOBAL awards_0_program_manager_nid String 50534
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Sequence data: The genomics of recovery from coral bleaching
PI: Stephen Palumbi
Data Version 1: 2019-03-18
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 2.2d 13 Jun 2019
attribute NC_GLOBAL date_created String 2019-03-18T18:31:46Z
attribute NC_GLOBAL date_modified String 2019-04-11T18:54:35Z
attribute NC_GLOBAL defaultDataQuery String &time
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.762497.1
attribute NC_GLOBAL Easternmost_Easting double -169.65462
attribute NC_GLOBAL geospatial_lat_max double -14.1795
attribute NC_GLOBAL geospatial_lat_min double -14.17977
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double -169.65462
attribute NC_GLOBAL geospatial_lon_min double -169.655
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/762497 (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 762540
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
attribute NC_GLOBAL keywords String accession, accession_link, bco, bco-dmo, biological, bleaching, bleaching_status, chemical, colony, data, dataset, date, dmo, erddap, latitude, link, longitude, management, oceanography, office, preliminary, sample, species, status, taxonomy, time
attribute NC_GLOBAL license String The data may be used and redistributed for free but is not intended
for legal use, since it may contain inaccuracies. Neither the data
Contributor, ERD, NOAA, nor the United States Government, nor any
of their employees or contractors, makes any warranty, express or
implied, including warranties of merchantability and fitness for a
particular purpose, or assumes any legal liability for the accuracy,
completeness, or usefulness, of this information.
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/762497 (external link)
attribute NC_GLOBAL Northernmost_Northing double -14.1795
attribute NC_GLOBAL param_mapping String {'762497': {'latitude': 'flag - latitude', 'longitude': 'flag - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/762497/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Stanford University
attribute NC_GLOBAL people_0_person_name String Dr Stephen R. Palumbi
attribute NC_GLOBAL people_0_person_nid String 51368
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 University of Western Australia
attribute NC_GLOBAL people_1_person_name String Luke Thomas
attribute NC_GLOBAL people_1_person_nid String 762507
attribute NC_GLOBAL people_1_role String Co-Principal Investigator
attribute NC_GLOBAL people_1_role_type String originator
attribute NC_GLOBAL people_2_affiliation String Stanford University
attribute NC_GLOBAL people_2_person_name String Dr Stephen R. Palumbi
attribute NC_GLOBAL people_2_person_nid String 51368
attribute NC_GLOBAL people_2_role String Contact
attribute NC_GLOBAL people_2_role_type String related
attribute NC_GLOBAL people_3_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_3_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_3_person_name String Amber York
attribute NC_GLOBAL people_3_person_nid String 643627
attribute NC_GLOBAL people_3_role String Data Manager
attribute NC_GLOBAL people_3_role_type String related
attribute NC_GLOBAL project String Ecological, evolutionary and physiological responses of corals to a mass bleaching event in American Samoa
attribute NC_GLOBAL projects_0_acronym String Bleaching American Samoa
attribute NC_GLOBAL projects_0_description String Description from NSF award abstract:
The strongest coral bleaching event in nearly 20 years began in American Samoa in January 2015. Coral bleaching occurs when ocean water temperatures exceed a coral's normal heat tolerance. But bleaching events usually show an unexplained pattern - colonies next to one another can show very different levels of bleaching - from pure white to the normal tan color of a healthy coral. The investigators have observed this pattern among 280 corals on reefs in American Samoa that have been studied for years. This system will be used to test four major hypotheses about what causes some corals to bleach and some not: differences in 1) species, 2) the temperature the corals experienced, 3) the symbiont they harbor, and 4) the genotype of the coral host. In addition, the investigators will return to American Samoa at regular intervals to measure the rate of recovery of each coral colony and conduct the same tests as above for recovery rate. The stark-white reefscapes left behind by bleaching events are one of the most common signals of increased ocean warming. This work will take advantage of years of prior study and the advent of a coral bleaching event to understand the rules for survival on reefs.
The reefs of American Samoa began showing a major bleaching event starting in January 2015, including 62 corals that have been intensively studied for coral thermal resistance, field temperatures, and symbiont type. In April 2015 the investigators monitored bleaching status of these and additional corals, totaling 280 corals from four species, and uncovered marked variation in bleaching extent within and between species and within and between reef regions. The team will test the relative importance of microclimate to bleaching state by examining records of approximately 50 temperature loggers in place since before the bleaching event. They will test the influence of symbiont type and host gene expression profiles by examining samples of 60 colonies taken at four time points after bleaching. The investigators will also examine the full suite of 280 corals for genetic variation to estimate the relationship between bleaching state, recovery rate and genetic polymorphism. These data will be used to test micro-climate, symbiont, and coral genetics as determinants of bleaching and bleaching recovery. Because the investigators have samples from these 280 colonies before bleaching mortality, this study will provide the first estimate for the evolutionary impact of a bleaching event on coral populations.
attribute NC_GLOBAL projects_0_end_date String 2017-06
attribute NC_GLOBAL projects_0_geolocation String American Samoa
attribute NC_GLOBAL projects_0_name String Ecological, evolutionary and physiological responses of corals to a mass bleaching event in American Samoa
attribute NC_GLOBAL projects_0_project_nid String 647914
attribute NC_GLOBAL projects_0_start_date String 2015-07
attribute NC_GLOBAL publisher_role String BCO-DMO Data Manager(s)
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL Southernmost_Northing double -14.17977
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v29
attribute NC_GLOBAL subsetVariables String species
attribute NC_GLOBAL summary String Coral colony genetic sequence accessions for samples collected from the lagoon environment of Ofu Island in the National Park of American Samoa between 2011 and 2015.
attribute NC_GLOBAL title String Coral colony genetic sequence accession numbers for samples collected from the lagoon environment of Ofu Island, American Samoa between 2011 and 2015.
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double -169.655
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.5-beta
variable sample   String  
attribute sample description String Sequence file (corresponds to NCBI library "Name" field for SRA sample)
attribute sample ioos_category String Unknown
attribute sample long_name String Sample
attribute sample units String unitless
variable date   String  
attribute date description String Year and Month the�colony was collected in format yyyy-mm
attribute date ioos_category String Time
attribute date long_name String Date
attribute date units String unitless
variable colony   String  
attribute colony description String colony label
attribute colony ioos_category String Unknown
attribute colony long_name String Colony
attribute colony units String unitless
variable bleaching_status   byte  
attribute bleaching_status _FillValue byte 127
attribute bleaching_status actual_range byte 0, 80
attribute bleaching_status description String Bleaching score (0-100% bleached)
attribute bleaching_status ioos_category String Unknown
attribute bleaching_status long_name String Bleaching Status
attribute bleaching_status units String percent (%)
variable accession   String  
attribute accession description String SRA Accession number at The National Center for Biotechnology Information
attribute accession ioos_category String Unknown
attribute accession long_name String Accession
attribute accession units String unitless
variable latitude   double  
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double -14.17977, -14.1795
attribute latitude axis String Y
attribute latitude colorBarMaximum double 90.0
attribute latitude colorBarMinimum double -90.0
attribute latitude description String Latitude of colony
attribute latitude ioos_category String Location
attribute latitude long_name String Latitude
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 -169.655, -169.65462
attribute longitude axis String X
attribute longitude colorBarMaximum double 180.0
attribute longitude colorBarMinimum double -180.0
attribute longitude description String Longitude of colony
attribute longitude ioos_category String Location
attribute longitude long_name String Longitude
attribute longitude standard_name String longitude
attribute longitude units String degrees_east
variable species   String  
attribute species description String Coral species (Genus species)
attribute species ioos_category String Taxonomy
attribute species long_name String Species
attribute species units String unitless
variable accession_link   String  
attribute accession_link description String SRA Accession link to The National Center for Biotechnology Information
attribute accession_link ioos_category String Unknown
attribute accession_link long_name String Accession Link
attribute accession_link units String untiless

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


 
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