|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|
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).
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)
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 )
|date||Month and year of sampling in format yyyy_mm||unitless|
|year||Year of sampleing||unitless|
|month||Month of sampling||unitless|
|Accession||Genetic accession number at NCBI||unitless|
|Accession_link||Link to genetic accession at NCBI||unitless|
|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.