Dataset: Coral colony sequece accessions: Hidden resilience to recurrent bleaching

Name: RNA sequence accession numbers for coral colonies that displayed a strong bleaching phenotype at Ofu Island, American Samoa between 2015 and 2016.
Published: 2019-03-18
Keywords: oceans

Cite This Dataset

DOI:10.1575/1912/bco-dmo.762511.2

Spatial Extent: N:-14.1799 E:-169.65448 S:-14.1799 W:-169.65448

Temporal Extent: 2015-04 - 2016-04

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)

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

RNA sequence accession numbers for coral colonies that displayed a strong bleaching phenotype at Ofu Island, American Samoa between 2015 and 2016.

Abstract:

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).

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2019-03-18	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.1575/1912/bco-dmo.762511.2	2019-04-26

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).

Methods & 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)

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 column of links to genetic accessions at NCBI

* Added separate year and month columns from parsing the Date column (format yyyy_mm )

Data Files

File
hidden.csv (Comma Separated Values (.csv), 4.94 KB) MD5:30102017f32034eab1e72a4dd236156e Primary data file for dataset ID 762511

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
year	Year of sampleing	unitless	year
sample	Sample identifier	unitless	sample
month	Month of sampling	unitless	month
date	Month and year of sampling in format yyyy_mm	unitless	no_bcodmo_term
Accession_link	Link to genetic accession at NCBI	unitless	external_link
Accession	Genetic accession number at NCBI	unitless	accession_number
species	Coral species	uniless	species
colony	Colony identifier	unitless	sample
bleaching_status	Bleaching status	percent	sample_descrip