|Palumbi, Stephen R.||Stanford University||Principal Investigator, Contact|
|Thomas, Luke||University of Western Australia||Co-Principal Investigator|
|York, Amber||Woods Hole Oceanographic Institution (WHOI BCO-DMO)||Data Manager|
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).
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.
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
|sample||Sequence file (corresponds to NCBI library "Name" field for SRA sample)||unitless|
|date||Year and Month the colony was collected in format yyyy-mm||unitless|
|bleaching_status||Bleaching score (0-100% bleached)||percent (%)|
|accession||SRA Accession number at The National Center for Biotechnology Information||unitless|
|latitude||Latitude of colony||decimal degrees|
|longitude||Longitude of colony||decimal degrees|
|species||Coral species (Genus species)||unitless|
|accession_link||SRA Accession link to The National Center for Biotechnology Information||untiless|
|Dataset-specific Instrument Name|| |
Illumina HiSeq 2500
|Generic Instrument Name|| |
Automated DNA Sequencer
|Generic Instrument 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.
|Start Date|| |
|End Date|| |
Coral colony samples, temperature, DNA/RNA, bleaching metrics.