Dataset Overview | National Centers for Environmental Information (NCEI)

RNA sequence accession numbers for coral colonies that displayed a strong bleaching phenotype at Ofu Island, American Samoa between 2015 and 2016 (NCEI Accession 0277948)

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This dataset contains biological and survey - biological data collected at American_Samoa during deployment Palumbi_AmSamoa_2013-2015 from 2015-04-01 to 2016-04-01. These data include species. The instruments used to collect these data include Automated DNA Sequencer. These data were collected by Dr Stephen R. Palumbi of Stanford University and Luke Thomas of University of Western Australia as part of the "Ecological, evolutionary and physiological responses of corals to a mass bleaching event in American Samoa (Bleaching American Samoa)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2019-04-26.

The following is the text of the dataset description provided by BCO-DMO:

Dataset Description:
This dataset includes accession numbers for 36 RNAseq libraries housed at The National Center for Biotechnology Information (NCBI). Coral colonies that displayed a strong bleaching phenotype at Ofu Island, American Samoa were sampled between 2015 and 2016.

The genetic accessions at NCBI referenced in this dataset will not be publicly accessible until 2019-05-01. This includes accession numbers and links to the accession page.

These data were published in Thomas & Palumbi (2017).

Dataset Citation

Cite as: Palumbi, Stephen R.; Thomas, Luke (2023). RNA sequence accession numbers for coral colonies that displayed a strong bleaching phenotype at Ofu Island, American Samoa between 2015 and 2016 (NCEI Accession 0277948). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0277948. Accessed [date].

Dataset Identifiers

ISO 19115-2 Metadata

gov.noaa.nodc:0277948

Full Text · XML

Download Data	HTTPS (download) Navigate directly to the URL for data access and direct download. FTP (download) These data are available through the File Transfer Protocol (FTP). FTP is no longer supported by most internet browsers. You may copy and paste the FTP link to the data into an FTP client (e.g., FileZilla or WinSCP).
Distribution Formats	TSV
Ordering Instructions	Contact NCEI for other distribution options and instructions.
Distributor	NOAA National Centers for Environmental Information +1-301-713-3277 NCEI.Info@noaa.gov
Dataset Point of Contact	NOAA National Centers for Environmental Information ncei.info@noaa.gov

Time Period	2015-04-01 to 2016-04-01
Spatial Bounding Box Coordinates	West: -169.65448 East: -169.65448 South: -14.1799 North: -14.1799
Spatial Coverage Map

General Documentation

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Descriptive Information
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Associated Resources

Biological, chemical, physical, biogeochemical, ecological, environmental and other data collected from around the world during historical and contemporary periods of biological and chemical oceanographic exploration and research managed and submitted by the Biological and Chemical Oceanography Data Management Office (BCO-DMO)
- NCEI Collection
  Navigate directly to the URL for data access and direct download.
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). Dataset version 2019-03-18. https://doi.org/10.1575/1912/bco-dmo.762511.2
- https://doi.org/10.1575/1912/bco-dmo.762511.2 (download)
  originator dataset

gov.noaa.nodc:BCO-DMO

Publication Dates	publication: 2023-05-06
Data Presentation Form	Digital table - digital representation of facts or figures systematically displayed, especially in columns
Dataset Progress Status	Complete - production of the data has been completed Historical archive - data has been stored in an offline storage facility
Data Update Frequency	As needed
Supplemental Information	Acquisition Description: 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)
Purpose	This dataset is available to the public for a wide variety of uses including scientific research and analysis.
Use Limitations	accessLevel: Public Distribution liability: NOAA and NCEI make no warranty, expressed or implied, regarding these data, nor does the fact of distribution constitute such a warranty. NOAA and NCEI cannot assume liability for any damages caused by any errors or omissions in these data. If appropriate, NCEI can only certify that the data it distributes are an authentic copy of the records that were accepted for inclusion in the NCEI archives.

Dataset Citation	Cite as: Palumbi, Stephen R.; Thomas, Luke (2023). RNA sequence accession numbers for coral colonies that displayed a strong bleaching phenotype at Ofu Island, American Samoa between 2015 and 2016 (NCEI Accession 0277948). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0277948. Accessed [date].
Cited Authors	Palumbi, Stephen R. Stanford University Thomas, Luke University of Western Australia
Principal Investigators	Stephen R. Palumbi Stanford University Luke Thomas University of Western Australia (UWA)
Contributors	Stanford University
Resource Providers	Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Points of Contact	Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Publishers	NOAA National Centers for Environmental Information
Acknowledgments	Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1547921 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1547921

Theme keywords	NODC DATA TYPES THESAURUS SPECIES IDENTIFICATION NODC OBSERVATION TYPES THESAURUS biological survey - biological WMO_CategoryCode oceanography BCO-DMO Standard Parameters accession number external_link month of year no standard parameter sample description sample identification species year Originator Parameter Names Accession Accession_link bleaching_status colony date month sample species year
Data Center keywords	NODC COLLECTING INSTITUTION NAMES THESAURUS Stanford University NODC SUBMITTING INSTITUTION NAMES THESAURUS Biological and Chemical Oceanography Data Management Office Global Change Master Directory (GCMD) Data Center Keywords BCO-DMO > Biological and Chemical Oceanography Data Management Office
Platform keywords	BCO-DMO Platform Names American_Samoa
Instrument keywords	BCO-DMO Standard Instruments Automated DNA Sequencer Originator Instrument Names Illumina HiSeq 2500
Place keywords	Provider Place Names American Samoa
Project keywords	BCO-DMO Standard Projects Ecological, evolutionary and physiological responses of corals to a mass bleaching event in American Samoa (Bleaching American Samoa) Provider Deployment IDs Palumbi_AmSamoa_2013-2015 Provider Funding Award Information Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1547921
Keywords	NCEI ACCESSION NUMBER 0277948

Use Constraints	Cite as: Palumbi, Stephen R.; Thomas, Luke (2023). RNA sequence accession numbers for coral colonies that displayed a strong bleaching phenotype at Ofu Island, American Samoa between 2015 and 2016 (NCEI Accession 0277948). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0277948. Accessed [date].
Data License	This dataset is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) License. SPDX License: Creative Commons Attribution 4.0 International (CC-BY-4.0)
Access Constraints	Use liability: NOAA and NCEI cannot provide any warranty as to the accuracy, reliability, or completeness of furnished data. Users assume responsibility to determine the usability of these data. The user is responsible for the results of any application of this data for other than its intended purpose.
Fees	In most cases, electronic downloads of the data are free. However, fees may apply for custom orders, data certifications, copies of analog materials, and data distribution on physical media.

Lineage information for: dataset
Processing Steps	2023-05-06T04:29:29Z - NCEI Accession 0277948 v1.1 was published.
Output Datasets	NCEI Accession 0277948 v1.1 NCEI Accession 0277948 v1.1 (download) published 2023-05-06T04:29:29Z

Last Modified: 2024-06-26T18:45:28Z
For questions about the information on this page, please email: ncei.info@noaa.gov

RNA sequence accession numbers for coral colonies that displayed a strong bleaching phenotype at Ofu Island, American Samoa between 2015 and 2016 (NCEI Accession 0277948)

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