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OAS accession Detail for 0277948, meta_version: 1. Current meta_version is: 1
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| accessions_id: | 0277948 | archive |
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| Title: | 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) |
| Abstract: | 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). |
| Date received: | 20190426 |
| Start date: | 20150401 |
| End date: | 20160401 |
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| West boundary: | -169.65448 |
| East boundary: | -169.65448 |
| North boundary: | -14.1799 |
| South boundary: | -14.1799 |
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| Submitting institution: | Biological and Chemical Oceanography Data Management Office |
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| Supplementary 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) |
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| Metadata version: | 1 |
| Keydate: | 2023-05-06 04:28:23+00 |
| Editdate: | 2023-05-06 04:28:46+00 |