The Ocean Archive System searches our original datasets as they were submitted to us, not individual points or profiles. If you want to search and retrieve ocean profiles in a common format, or objectively analyzed fields, your better option may be to use one of our project applications. See: Access Data
OAS accession Detail for 0292017
| << previous | |revision: 1 |
| accessions_id: | 0292017 | archive |
|---|---|
| Title: | NCBI accession numbers for RNAseq data from five coral species experimentally exposed to Stony Coral Tissue Loss Disease (SCTLD) at the University of the Virgin Islands in 2019 (NCEI Accession 0292017) |
| Abstract: | This dataset contains biological and survey - biological data collected in the Caribbean Sea from 2019-03-17 to 2019-04-12. These data include species. The instruments used to collect these data include Automated DNA Sequencer and Qiagen TissueLyser II. These data were collected by Laura Mydlarz of University of Texas at Arlington as part of the "RAPID: Collaborative Research: Predicting the Spread of Multi-Species Coral Disease Using Species Immune Traits (Multi-Species Coral Disease)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2022-10-05. The following is the text of the dataset description provided by BCO-DMO: NCBI accession numbers for RNAseq data from five coral species experimentally exposed to SCTLD Dataset Description: Acquisition Description: A Stony Coral Tissue Loss Disease (SCTLD) transmission experiment was carried out at the University of the Virgin Islands (UVI) in April of 2019 and is described in Meiling et al. (2021). Coral colonies were collected from Rupert's Rock Reef (18.3277 N, -64.926 E) from March 17 to April 02 of 2019. One fragment from five species of stony coral was placed into a control mesocosm equidistant from a central healthy coral colony. Corresponding genet fragments were placed into an experimental mesocosm equidistant from a SCTLD-infected coral colony. This paired design was replicated for a total of 8 genets per species. Experimental coral fragments that developed lesions were removed and stored at -80ºC for RNA sequencing when 30% tissue loss was achieved. Corresponding control coral fragments were removed and stored at the same time. Tissue samples were harvested from the fragments and total RNA was extracted using the RNAqeous-4PCR total RNA isolation kit (Invitrogen, Life Technologies AM1914) as explained in Veglia et al. (2022). Tissues were lysed using a refrigerated Qiagen TissueLyser II microcentrifuge at 30 oscillations per second for 30 seconds. Contaminating DNA and chromatin were removed from the total RNA using the Ambion DNase I (RNase-free) kit (Invitrogen, Life Technologies AM2222). Samples were preprocessed by Novogene Co., Ltd. for mRNA enrichment using polyA tail capture; the mRNA libraries underwent 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 instrument using the NEBNext Ultra II RNA library prep kit. |
| Date received: | 20221005 |
| Start date: | 20190317 |
| End date: | 20190412 |
| Seanames: | |
| West boundary: | -64.926 |
| East boundary: | -64.926 |
| North boundary: | 18.328 |
| South boundary: | 18.328 |
| Observation types: | |
| Instrument types: | |
| Datatypes: | |
| Submitter: | |
| Submitting institution: | Biological and Chemical Oceanography Data Management Office |
| Collecting institutions: | |
| Contributing projects: | |
| Platforms: | |
| Number of observations: | |
| Supplementary information: | |
| Availability date: | |
| Metadata version: | 1 |
| Keydate: | 2024-04-29 15:51:37+00 |
| Editdate: | 2024-04-29 15:52:11+00 |