http://lod.bco-dmo.org/id/dataset/762511
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
2019-03-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
RNA sequence accession numbers for coral colonies that displayed a strong bleaching phenotype at Ofu Island, American Samoa between 2015 and 2016.
2019-03-18
publication
2019-03-18
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-04-26
publication
https://doi.org/10.1575/1912/bco-dmo.762511.2
Stephen R. Palumbi
Stanford University
principalInvestigator
Luke Thomas
University of Western Australia
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: Palumbi, S., Thomas, L. (2019) RNA sequence accession numbers for coral colonies that displayed a strong bleaching phenotype at Ofu Island, American Samoa between 2015 and 2016. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2019-03-18 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.762511.2 [access date]
Dataset Description: <p>This dataset includes accession numbers for 36 RNAseq libraries housed at&nbsp;The National Center for Biotechnology Information (NCBI).&nbsp; Coral colonies that displayed a strong bleaching phenotype at Ofu Island, American Samoa were sampled between 2015 and 2016.&nbsp;<br />
<br />
The genetic accessions at NCBI referenced in this dataset will not be publicly accessible until&nbsp;2019-05-01.&nbsp; &nbsp;This includes accession numbers and links to the accession page.<br />
<br />
These data were published in Thomas &amp; Palumbi (2017).&nbsp; &nbsp;</p> Methods and Sampling: Colonies that displayed a strong bleaching phenotype in April 2015 were selected for transcriptome-wide gene expression analyses. These colonies were subsequently sampled in August 2015, December 2015 and April 2016. For these 36 field-collected tissue samples (five colonies of A. gemmifera and four colonies of A. hyacinthus across four sample dates), total RNA was extracted Qiagens RNAeasy Plus Kit. In total 36 cDNA libraries were generated using the Illumina TruSeq RNA Library Prep Kit v2 with Protoscript II Reverse Transcriptase. We carried out multiplexed Illumina sequencing at the University of Utah Microarray and Genomic Analysis Core Facility. Fastq files were mapped to a reference transcriptome (Barshis et al., 2013) using HISAT2 (Langmead & Salzberg, 2012) with a minimum mapping quality of 10. We used SAMtools (Li et al., 2009) to generate counts for each contig in our reference transcriptome. Counts matrices were normalized in DESeq2.0 (Love, Huber, & Anders, 2014).
Approximate coordinates for this dataset are "Pool 400", back reef lagoon, Ofu, American Samoa (-14.17990, -169.65448)
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1547921 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1547921
completed
Stephen R. Palumbi
Stanford University
831-655-6214
Hopkins Marine Station 120 Ocean View Blvd
Pacific Grove
CA
93950
USA
spalumbi@stanford.edu
pointOfContact
Luke Thomas
University of Western Australia
luke.thomas@uwa.edu.au
pointOfContact
asNeeded
Dataset Version: 2
Unknown
sample
colony
species
date
year
month
bleaching_status
Accession
Accession_link
Illumina HiSeq 2500
theme
None, User defined
sample identification
species scientific name (binomial)
No BCO-DMO term
year
month of year
sample description
accession number
external_link
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
Palumbi_AmSamoa_2013-2015
service
Deployment Activity
American Samoa
place
Locations
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.
Ecological, evolutionary and physiological responses of corals to a mass bleaching event in American Samoa
https://osprey.bco-dmo.org/project/647914
Ecological, evolutionary and physiological responses of corals to a mass bleaching event in American Samoa
<p><em>Description from NSF award abstract:</em><br />
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.</p>
<p>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.</p>
Bleaching American Samoa
largerWorkCitation
project
eng; USA
oceans
American Samoa
-169.65448
-169.65448
-14.1799
-14.1799
2015-04-01
2016-04-01
American Samoa
0
BCO-DMO catalogue of parameters from RNA sequence accession numbers for coral colonies that displayed a strong bleaching phenotype at Ofu Island, American Samoa between 2015 and 2016.
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/765345.rdf
Name: sample
Units: unitless
Description: <p>Sample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/765346.rdf
Name: colony
Units: unitless
Description: <p>Colony identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/765347.rdf
Name: species
Units: uniless
Description: <p>Coral species</p>
http://lod.bco-dmo.org/id/dataset-parameter/765348.rdf
Name: date
Units: unitless
Description: <p>Month and year of sampling in format yyyy_mm</p>
http://lod.bco-dmo.org/id/dataset-parameter/765349.rdf
Name: year
Units: unitless
Description: <p>Year of sampleing</p>
http://lod.bco-dmo.org/id/dataset-parameter/765350.rdf
Name: month
Units: unitless
Description: <p>Month of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/765351.rdf
Name: bleaching_status
Units: percent
Description: <p>Bleaching status</p>
http://lod.bco-dmo.org/id/dataset-parameter/765352.rdf
Name: Accession
Units: unitless
Description: <p>Genetic accession number at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/765353.rdf
Name: Accession_link
Units: unitless
Description: <p>Link to genetic accession 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
5060
https://darchive.mblwhoilibrary.org/bitstream/1912/24075/1/dataset-762511_coral-colony-sequece-accessions-hidden-resilience-recurrent-bleaching__v2.tsv
download
https://doi.org/10.1575/1912/bco-dmo.762511.2
download
onLine
dataset
Colonies that displayed a strong bleaching phenotype in April 2015 were selected for transcriptome-wide gene expression analyses. These colonies were subsequently sampled in August 2015, December 2015 and April 2016. For these 36 field-collected tissue samples (five colonies of A. gemmifera and four colonies of A. hyacinthus across four sample dates), total RNA was extracted Qiagens RNAeasy Plus Kit. In total 36 cDNA libraries were generated using the Illumina TruSeq RNA Library Prep Kit v2 with Protoscript II Reverse Transcriptase. We carried out multiplexed Illumina sequencing at the University of Utah Microarray and Genomic Analysis Core Facility. Fastq files were mapped to a reference transcriptome (Barshis et al., 2013) using HISAT2 (Langmead & Salzberg, 2012) with a minimum mapping quality of 10. We used SAMtools (Li et al., 2009) to generate counts for each contig in our reference transcriptome. Counts matrices were normalized in DESeq2.0 (Love, Huber, & Anders, 2014).
Approximate coordinates for this dataset are "Pool 400", back reef lagoon, Ofu, American Samoa (-14.17990, -169.65448)
Specified by the Principal Investigator(s)
<div>BCO-DMO Data Manager Processing Notes:</div>
<div>* added a conventional header with dataset name, PI name, version date</div>
<div>* modified parameter names to conform with BCO-DMO naming conventions</div>
<div>* added column of links to genetic accessions at NCBI</div>
<div>* Added separate year and month columns from parsing the Date column (format yyyy_mm )</div>
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
Illumina HiSeq 2500
PI Supplied Instrument Name: Illumina HiSeq 2500 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.
Deployment: Palumbi_AmSamoa_2013-2015
Palumbi_AmSamoa_2013-2015
American_Samoa
island
Palumbi_AmSamoa_2013-2015
Stephen R. Palumbi
Stanford University
American_Samoa
island