BCO-DMO ERDDAP
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Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv
attribute NC_GLOBAL acquisition_description String Colonies that displayed a strong bleaching phenotype in April 2015 were\nselected for transcriptome-wide gene expression analyses. These colonies were\nsubsequently sampled in August 2015, December 2015 and April 2016. For these\n36 field-collected tissue samples (five colonies of A. gemmifera and four\ncolonies of A. hyacinthus across four sample dates), total RNA was extracted\nQiagens RNAeasy Plus Kit. In total 36 cDNA libraries were generated using the\nIllumina TruSeq RNA Library Prep Kit v2 with Protoscript II Reverse\nTranscriptase. We carried out multiplexed Illumina sequencing at the\nUniversity of Utah Microarray and Genomic Analysis Core Facility. Fastq files\nwere mapped to a reference transcriptome (Barshis et al., 2013) using HISAT2\n(Langmead & Salzberg, 2012) with a minimum mapping quality of 10. We used\nSAMtools (Li et al., 2009) to generate counts for each contig in our reference\ntranscriptome. Counts matrices were normalized in DESeq2.0 (Love, Huber, &\nAnders, 2014).\n \nApproximate coordinates for this dataset are \"Pool 400\", back reef lagoon,\nOfu, American Samoa (-14.17990, -169.65448)
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 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 accessions: Hidden resilience to recurrent bleaching \n  PI: Stephen Palumbi \n  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 2.3  19 Dec 2019
attribute NC_GLOBAL date_created String 2019-03-18T18:45:27Z
attribute NC_GLOBAL date_modified String 2019-04-26T21:24:46Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.762511.2
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/762511 (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 762537
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, link, management, month, oceanography, office, preliminary, sample, species, status, year
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/762511/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/762511 (external link)
attribute NC_GLOBAL param_mapping String {'762511': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/762511/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Stanford University
attribute NC_GLOBAL people_0_person_name String 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 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 Bleaching American Samoa
attribute NC_GLOBAL projects_0_acronym String Bleaching American Samoa
attribute NC_GLOBAL projects_0_description String Description from NSF award abstract:\nThe 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.\nThe 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_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 standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL summary String RNA sequence accession numbers for coral colonies that displayed a strong bleaching phenotype at Ofu Island, American Samoa between 2015 and 2016. This dataset includes accession numbers for 36 RNAseq libraries housed at The National Center for Biotechnology Information (NCBI).
attribute NC_GLOBAL title String [Coral colony sequece accessions: Hidden resilience to recurrent bleaching] - RNA sequence accession numbers for coral colonies that displayed a strong bleaching phenotype at Ofu Island, American Samoa between 2015 and 2016. (Ecological, evolutionary and physiological responses of corals to a mass bleaching event in American Samoa)
attribute NC_GLOBAL version String 2
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable sample String
attribute sample bcodmo_name String sample
attribute sample description String Sample identifier
attribute sample long_name String Sample
attribute sample nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute sample units String unitless
variable colony String
attribute colony bcodmo_name String sample
attribute colony description String Colony identifier
attribute colony long_name String Colony
attribute colony nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute colony units String unitless
variable species String
attribute species bcodmo_name String species
attribute species description String Coral species
attribute species long_name String Species
attribute species units String uniless
variable date String
attribute date bcodmo_name String unknown
attribute date description String Month and year of sampling in format yyyy_mm
attribute date long_name String Date
attribute date units String unitless
variable year short
attribute year _FillValue short 32767
attribute year actual_range short 2015, 2016
attribute year bcodmo_name String year
attribute year description String Year of sampleing
attribute year long_name String Year
attribute year nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/ (external link)
attribute year units String unitless
variable month String
attribute month bcodmo_name String month
attribute month description String Month of sampling
attribute month long_name String Month
attribute month nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/MNTHXXXX/ (external link)
attribute month units String unitless
variable bleaching_status byte
attribute bleaching_status _FillValue byte 127
attribute bleaching_status actual_range byte 0, 100
attribute bleaching_status bcodmo_name String sample_descrip
attribute bleaching_status description String Bleaching status
attribute bleaching_status long_name String Bleaching Status
attribute bleaching_status units String percent
variable Accession String
attribute Accession bcodmo_name String accession number
attribute Accession description String Genetic accession number at NCBI
attribute Accession long_name String Accession
attribute Accession units String unitless
variable Accession_link String
attribute Accession_link bcodmo_name String external_link
attribute Accession_link description String Link to genetic accession at NCBI
attribute Accession_link long_name String Accession Link
attribute Accession_link units String unitless

 
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