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Location:\u00a0Brewer\u2019s Bay (18.34403, -64.98435), St. Thomas, The U.S. Virgin Islands<\/p>\n
Processing of fragments included freezing the coral tissue in liquid nitrogen and storing at -80\u02daC for 16S rRNA analysis. DNA from the coral samples were extracted at the University of Texas at Arlington (UTA) using DNeasy Powersoil Isolation kits (MO BIO Laboratories, Carlsbad, CA).\u00a0 Roughly 0.25g of tissue was removed from each of the coral fragments. Tissue from healthy-state fragments (\u201ccontrol\u201d) was extracted from the center of the fragment. Tissue was extracted in a similar manner from fragments exposed to WPD that did not display lesions by the end of the experiment (\u201cdisease-exposed\u201d). For fragments that developed a lesion(s) (\u201cdisease-infected\u201d), tissue was extracted approximately 2 to 3mm horizontally from the lesion margin.\u00a0\u00a0<\/p>\n
Tissue samples were sent to MR DNA Molecular Research LP (Shallowater, TX) for 16S rRNA gene amplification using 515F and 806R primers for the V4 region and sequenced on an Illumina MiSeq 2x250bp PE reads. Before sequencing, coral DNA was amplified using 515F and 806R primers through 30 PCR cycles using HotStarTaq Plus Master Mix Kit (Qiagen, USA) under the following conditions: 94\u00b0C for 3 minutes, followed by 30-35 cycles of 94\u00b0C for 30 seconds, 53\u00b0C for 40 seconds and 72\u00b0C for 1 minute, after which a final elongation step at 72\u00b0C for 5 minutes was performed. PCR products were checked for amplification intensity and integrity on a 2% agarose gel and then bands of similar weight were pooled, purified using Ampure XP beads and used for illumina DNA library prep. Libraries were sequenced at MR DNA on an illumina MiSeq and then bioinformatically processed to combine homologous sequences, depleted barcodes, sequences <150bp removed, and sequences with ambiguous base calls removed using the MR DNA analysis pipeline (MR DNA, Shallowater, TX, USA).\u00a0<\/p>\n
Libraries were sequenced at MR DNA on an illumina MiSeq and then bioinformatically processed to combine homologous sequences, depleted barcodes, sequences <150bp removed, and sequences with ambiguous base calls removed using the MR DNA analysis pipeline (MR DNA, Shallowater, TX, USA). Sequences were grouped into operational taxonomic units (OTU\u2019s) with a 3% tolerated divergence (97% similarity) and taxonomically annotated using BLASTn against the NCBI database.
\n\u200b
\nInstruments:\u00a0
\nDNeasy Powersoil Isolation kits (MO BIO Laboratories, Carlsbad, CA)
\nIllumina MiSeq 2x250bp PE reads
\nHotStarTaq Plus Master Mix Kit (Qiagen, USA)
\nMR DNA analysis pipeline (MR DNA, Shallowater, TX, USA)
\nTaxonomically annotated using BLASTn against the NCBI database<\/p>\n
Coral species list in this dataset:<\/p>\n
ScientificName,AphiaID<\/strong> Sequence data referenced in this dataset can be found in the NCBI SRA database under the National Center for Biotechnology Information BioProject PRJNA667272.\u00a0<\/p><\/div>","@type":"rdf:HTML"}],"http:\/\/www.w3.org\/2000\/01\/rdf-schema#label":[{"@value":"Coral 16s rRNA","@type":"xsd:string"}],"http:\/\/ocean-data.org\/schema\/hasProcessingDescription":[{"@value":" BCO-DMO data manager processing notes:
\nColpophyllia natans,289697
\nMontastraea cavernosa,287962
\nOrbicella annularis,758260
\nOrbicella faveolata,758261
\nPorites astreoides,288889
\nPorites porites,207238
\nSiderastrea siderea,207516<\/p><\/div>","@type":"rdf:HTML"}],"http:\/\/purl.org\/dc\/terms\/description":[{"@value":"
\n* Data submitted in file\u00a0BCO DMO EAGER Microbiome metadata.xlsx sheet 1 extracted to csv
\n* Modified parameter names to conform with BCO-DMO naming conventions: only A-Za-z0-9 and underscore allowed.\u00a0 Can not start with a number.\u00a0 (spaces, +, and - changed to underscores).\u00a0
\n* Unique species list of species names in this dataset checked using the World Register of Marine Species (WoRMS) taxa match tool.\u00a0 All names were exact matches to accepted names as of 2021-02-17.\u00a0 Species list and AphiaIDs added to the metadata.
\n* \"sample_title\" column had no values so it was removed from the dataset.
\n*\u00a0 The combined lat_lon e.g. values \"18.34 N 64.98 W\" were removed\u00a0 and separate columns for latitude and longitude were added in decimal degrees using the value provided in the metadata.\u00a0
\n* commas in geolocation replaced with semicolons. \"USA: St thomas, Brewer's Bay\" changed to \"USA: St thomas; Brewer's Bay\"<\/p><\/div>","@type":"rdf:HTML"}],"http:\/\/purl.org\/dc\/terms\/identifier":[{"@value":"841008","@type":"xsd:int"}],"http:\/\/purl.org\/dc\/terms\/title":[{"@value":"Coral 16s rRNA"}],"http:\/\/purl.org\/dc\/terms\/date":[{"@value":"2021-02-17T17:40:26-05:00","@type":"xsd:dateTime"}],"http:\/\/purl.org\/dc\/terms\/created":[{"@value":"2021-02-17T17:40:26-05:00","@type":"xsd:dateTime"}],"http:\/\/purl.org\/dc\/terms\/modified":[{"@value":"2021-02-17T19:07:04-05:00","@type":"xsd:dateTime"}],"http:\/\/rdfs.org\/ns\/void#inDataset":[{"@id":"http:\/\/www.bco-dmo.org\/"}],"http:\/\/ocean-data.org\/schema\/namedGraph":[{"@value":"urn:bcodmo:dataset:841008","@type":"xsd:token"}],"http:\/\/ocean-data.org\/schema\/osprey_page":[{"@id":"https:\/\/www.bco-dmo.org\/dataset\/841008"}],"http:\/\/ocean-data.org\/schema\/identifier":[{"@value":"_:Identifier841008"}],"http:\/\/ocean-data.org\/schema\/datasetTitle":[{"@value":"Coral 16s rRNA sequence accession, sample, and experimental treatment information from white plague disease exposed corals at Brewer\u2019s Bay, St. Thomas, The U.S. Virgin Islands in June of 2017","@language":"en-US"}],"http:\/\/ocean-data.org\/schema\/abstract":[{"@value":"Coral 16s rRNA sequence accession, sample, and experimental treatment information from white plague disease exposed corals. Seven Caribbean coral species were exposed to white plague at Brewer\u2019s Bay, St. Thomas, The U.S. Virgin Islands in June of 2017. \r\n\r\nSequence data can be found in the NCBI SRA database under the National Center for Biotechnology Information BioProject PRJNA667272.","@language":"en-US"}],"http:\/\/purl.org\/dc\/terms\/rights":[{"@id":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"http:\/\/ocean-data.org\/schema\/deprecated":[{"@value":"false","@type":"xsd:boolean"}],"http:\/\/ocean-data.org\/schema\/temporalExtent":[{"@value":"_:temporalExtent841008"}],"http:\/\/ocean-data.org\/schema\/spatialCoverage":[{"@value":"_:spatialCoverage841008"}],"http:\/\/purl.org\/dc\/terms\/bibliographicCitation":[{"@value":"Mydlarz, L., Brandt, M. (2021) Coral 16s rRNA sequence accession, sample, and experimental treatment information from white plague disease exposed corals at Brewer\u2019s Bay, St. Thomas, The U.S. Virgin Islands in June of 2017. 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