ERDDAP > info > bcodmo_dataset_762497

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	FGDC, ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
	set	data	graph		files	public	[Coral colony sequence accessions: The genomics of recovery from coral bleaching] - Coral colony genetic sequence accession numbers for samples collected from the lagoon environment of Ofu Island, American Samoa between 2011 and 2015. (Ecological, evolutionary and physiological responses of corals to a mass bleaching event in American Samoa)		F   I   M	background			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
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 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/
attribute	NC_GLOBAL	data_source	String	extract_data_as_tsv version 2.3 19 Dec 2019
attribute	NC_GLOBAL	date_created	String	2019-03-18T18:31:46Z
attribute	NC_GLOBAL	date_modified	String	2019-04-11T18:54:35Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
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
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
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/762497/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/762497
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
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: 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_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	-14.17977
attribute	NC_GLOBAL	standard_name_vocabulary	String	CF Standard Name Table v55
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 sequence accessions: The genomics of recovery from coral bleaching] - Coral colony genetic sequence accession numbers for samples collected from the lagoon environment of Ofu Island, American Samoa between 2011 and 2015. (Ecological, evolutionary and physiological responses of corals to a mass bleaching event in American Samoa)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	Westernmost_Easting	double	-169.655
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	sample		String
attribute	sample	bcodmo_name	String	sample
attribute	sample	description	String	Sequence file (corresponds to NCBI library "Name" field for SRA sample)
attribute	sample	long_name	String	Sample
attribute	sample	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	sample	units	String	unitless
variable	date		String
attribute	date	bcodmo_name	String	Date_Month
attribute	date	description	String	Year and Month the colony was collected in format yyyy-mm
attribute	date	long_name	String	Date
attribute	date	units	String	unitless
variable	colony		String
attribute	colony	bcodmo_name	String	sample
attribute	colony	description	String	colony label
attribute	colony	long_name	String	Colony
attribute	colony	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
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	bcodmo_name	String	bleach_percent
attribute	bleaching_status	description	String	Bleaching score (0-100% bleached)
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	SRA Accession number at The National Center for Biotechnology Information
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	bcodmo_name	String	latitude
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	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P09/current/LATX/
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	bcodmo_name	String	longitude
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	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P09/current/LONX/
attribute	longitude	standard_name	String	longitude
attribute	longitude	units	String	degrees_east
variable	species		String
attribute	species	bcodmo_name	String	species
attribute	species	description	String	Coral species (Genus species)
attribute	species	long_name	String	Species
attribute	species	units	String	unitless
variable	accession_link		String
attribute	accession_link	bcodmo_name	String	external_link
attribute	accession_link	description	String	SRA Accession link to The National Center for Biotechnology Information
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, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.