Dataset: Coral colony sequence accessions: The genomics of recovery from coral bleaching

Name: Coral colony genetic sequence accession numbers for samples collected from the lagoon environment of Ofu Island, American Samoa between 2011 and 2015.
Published: 2019-03-18
Keywords: oceans

Cite This Dataset

DOI:10.1575/1912/bco-dmo.762497.1

Spatial Extent: N:-14.1795 E:-169.65462 S:-14.17977 W:-169.655

Temporal Extent: 2011-04 - 2015-12

Project:

Ecological, evolutionary and physiological responses of corals to a mass bleaching event in American Samoa (Bleaching American Samoa)

Principal Investigator:

Stephen R. Palumbi (Stanford University)

Co-Principal Investigator:

Luke Thomas (University of Western Australia)

Contact:

Stephen R. Palumbi (Stanford University)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2019-03-18

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Coral colony genetic sequence accession numbers for samples collected from the lagoon environment of Ofu Island, American Samoa between 2011 and 2015.

Abstract:

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.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2019-03-18	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.1575/1912/bco-dmo.762497.1	2019-04-12

Description

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. All data and samples were collected at depths less than 3.0m.

This dataset includes all sequence data accession numbers for the publication Thomas & Palumbi (2017) housed at The National Center for Biotechnology Information under BioProject PRJNA522016 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA522016).

Methods & Sampling

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.

Data Processing Description

BCO-DMO Data Manager Processing Notes:

* added a conventional header with dataset name, PI name, version date

* modified parameter names to conform with BCO-DMO naming conventions
* added lat/lons and species name for each coral colony from information provided with a previous data submission for coral colony water temps: https://www.bco-dmo.org/dataset/676132
* added a data column for direct links to NCBI accession numbers

Data Files

File
recovery.csv (Comma Separated Values (.csv), 4.42 KB) MD5:8bb3c990e6282366f793038d919c04e4 Primary data file for dataset ID 762497

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1547921

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
Palumbi_AmSamoa_2013-2015		2013-01-04	American_Samoa	Stephen R. Palumbi (Principal Investigator)	data info

Instruments

Automated DNA Sequencer

Supplied Name: Illumina HiSeq 2500

Supplied Description:

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

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.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
sample	Sequence file (corresponds to NCBI library "Name" field for SRA sample)	unitless	sample
date	Year and Month the colony was collected in format yyyy-mm	unitless	Date_Month
colony	colony label	unitless	sample
bleaching_status	Bleaching score (0-100% bleached)	percent (%)	bleach_percent
accession	SRA Accession number at The National Center for Biotechnology Information	unitless	accession_number
latitude	Latitude of colony	decimal degrees	lat
longitude	Longitude of colony	decimal degrees	lon
species	Coral species (Genus species)	unitless	species
accession_link	SRA Accession link to The National Center for Biotechnology Information	untiless	external_link