http://lod.bco-dmo.org/id/dataset/924760 eng; USA utf8 dataset Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 2024-04-09 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Acropora cervicornis transcriptomes: nutrient- and disease-exposed from samples collected at Mote Marine Laboratory in situ nursery from June to July 2022 2026-09-11 publication 2026-09-11 revision Woods Hole Oceanographic Institution (WHOI BCO-DMO) 2026-09-11 publication https://doi.org/10.26008/1912/bco-dmo.924760.1 Rebecca Vega Thurber Oregon State University principalInvestigator Erinn M. Muller Mote Marine Laboratory principalInvestigator Grace J. Klinges Mote Marine Laboratory principalInvestigator Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. publisher Cite this dataset as: Klinges, G. J., Muller, E. M., Vega Thurber, R. (2026) Acropora cervicornis transcriptomes: nutrient- and disease-exposed from samples collected at Mote Marine Laboratory in situ nursery from June to July 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-09-11 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.924760.1 [access date] Acropora cervicornis transcriptomes: nutrient- and disease-exposed Dataset Description: Methods and Sampling: &lt;p&gt;Samples of coral tissue, skeleton, and mucus were taken from two genotypes of &lt;em&gt;Acropora cervicornis&lt;/em&gt; prior to nutrient enrichment (n = 20 per genotype), prior to disease exposure (n = 18 per genotype), and at various stages during disease development. The samples&amp;nbsp;were collected at the Mote Marine Laboratory in situ nursery from June to July 2022. All surviving ramets at one week after disease exposure were sampled. To sample each coral, 6-8 polyps were excised using a flame-sterilized blade and placed in a 1.5mL microcentrifuge tube containing 1mL of DNA/RNA shield (Zymo Research, R1100-250, Irvine, CA, USA). Samples were transferred to a -80℃ freezer for long-term storage. In preparation for RNA extractions, the samples were removed from the -80℃ freezer and thawed on ice. With flame-sterilized tweezers, half of the biomass was transferred to a Disruptor Tube (Omega Bio-Tek, Norcross, GA, USA), the other half was kept as a bioarchive and returned to -80℃. RNA from each sample was isolated utilizing the E.Z.N.A. DNA/RNA Isolation Kit (Omega Bio-Tek, Norcross, GA, USA) with slight modifications to the manufacturer’s protocol to increase yield. RNA isolates were stored at -80℃. DNA quantity and quality was assessed utilizing a NanoDrop spectrophotometer (Thermo Fisher Scientific™, Waltham, MA, USA). Samples were shipped on dry ice to the&amp;nbsp;Oklahoma Medical Research Foundation NGS Core, where RNA cleanup, precipitation, and polyA selection was performed.&amp;nbsp; Libraries were prepared using the IDT xGen RNA Library kit. Final QC was performed using KAPA qPCR and Agilent Tapestation to confirm rRNA content, and libraries were sequenced on a NovaSeq 6000 using S4 chemistry.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1923836 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1923836 Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1923926 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1923926 completed Rebecca Vega Thurber Oregon State University rvegathurber@gmail.com pointOfContact Erinn M. Muller Mote Marine Laboratory 941-388-4441 x 310 1600 Ken Thompson Parkway Sarasota FL 34241 USA emuller@mote.org pointOfContact Grace J. Klinges Mote Marine Laboratory Center for Global Discovery and Conservation Science Tempe AZ USA gklinges@asu.edu pointOfContact asNeeded Dataset Version: 1 Unknown rnaseq_name sample_name sample_title BioSample BioProject organism tissue isolation_source geo_loc_name lat lon collection_date isolate Genotype Treatment Exposure Disease_exposure Health_status group title design_description platform instrument_model library_name library_strategy library_source library_selection library_layout filetype filename filename2 Illumina Nova Seq 6000 theme None, User defined sample identification NCBI BioSample accession NCBI BioProject accession animal group (category) sample description region latitude longitude date seq_descrip instrument instrument model datatype file_name featureType BCO-DMO Standard Parameters Automated DNA Sequencer Thermo Scientific NanoDrop spectrophotometer instrument BCO-DMO Standard Instruments otherRestrictions otherRestrictions Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use. Collaborative Research: Tracking the interacting roles of the environment, host genotype, and a novel Rickettsiales in coral disease susceptibility https://osprey.bco-dmo.org/project/820022 Collaborative Research: Tracking the interacting roles of the environment, host genotype, and a novel Rickettsiales in coral disease susceptibility <p><em>NSF Award Abstract:</em><br /> Historically one of the most abundant reef-building corals in Florida and the wider Caribbean, the staghorn coral, <em>Acropora cervicornis</em>, is now listed as critically endangered primarily because of previous and reoccurring disease events. Understanding the holistic mechanisms of disease susceptibility in this coral is a top concern of practitioners engaged in conservation and restoration. The investigators recently discovered a group of parasitic bacteria common within the microbial community of <em>A. cervicornis</em> that can reduce the growth and health of corals when reefs are exposed to nutrient polluted waters. Determining how interactions among the coral host, this parasitic microbe, and the environment are linked to disease susceptibility provides critical insight and greater success of future restoration efforts. Yet the complexity of animal microbiomes and the contextual nature of disease make it difficult to identify the specific cause of many disease outbreaks. In this project, the investigators conduct experiments to explore the interactions among different genetic strains of coral and these bacteria in various nutrient scenarios to better understand how this bacterium affects the susceptibility of staghorn coral to diseases. This project also characterizes the genomics, host range, and local and global distribution of this bacterial coral parasite to determine how its evolutionary history and physiology drive disease susceptibility in this important coral species. The project trains two postdocs, one technician, and seven students (one graduate, six undergraduates) in integrative sciences that span marine science, physiology, genetics, microbiology, omics, and statistical modeling. A research-based after school program in Florida is expanded to include microbiology and create a new program module called Microbial warriors, with a focus on women in science. The investigators produce documentary style films and outreach materials to broadly communicate the project science and conservation efforts to local and national communities via presentations at Mote Marine Lab and the Oregon Museum of Science and Industry. This project is co-funded by the Biological Oceanography Program in the Division of Ocean Sciences and the Symbiosis, Defense, and Self-recognition Program in the Division of Integrative Organismal Systems.</p> <p>The investigators recently identified a marine <em>Rickettsiales</em> bacterium that, in corals, can be stimulated to grow in the presence of elevated nitrogen and phosphorous species. Based on genomic reconstruction and phylogeography, this bacteria is classified as a novel bacterial genus, <em>Candidatus Aquarickettsia</em>, and showed that it is broadly associated with scleractinian corals worldwide. Importantly, using a model system, the endangered <em>Acropora cervicornis</em> coral, the team has also shown that the growth of this bacterium in vivo is associated with reduced host growth and increased disease susceptibility. This project aims to more completely evaluate the mechanisms behind and impacts of these inducible infections on coral physiology and host-bacterial symbiosis. The investigators conduct nutrient dosing experiments on different coral genotypes with various <em>Rickettsiales</em> abundances. Using a range of omics and microscopy techniques, the team quantifies the resulting effects on holobiont phenotypes. The investigators are also comparing the genomes of these bacteria in the different Acroporid hosts and other coral genera to evaluate facets of the bacterium's evolutionary history, as well as to identify possible mechanisms of its proliferation, virulence, and host specificity. This interdisciplinary project mechanistically links nutrients to temporal changes in host, algal symbiont, and bacterial parasite physiology and also explain why there is natural variation in these responses by exploring how host and parasite genotypes and growth dynamics combined with environmental contextuality alter holobiont phenotypes.</p> <p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p> Coral Rickettsiales largerWorkCitation project eng; USA oceans -81.40009 -81.40009 24.56257 24.56257 2022-06-29 2022-07-27 at Oregon State University and in the Florida Keys at Mote Marine Laboratory 0 BCO-DMO catalogue of parameters from Acropora cervicornis transcriptomes: nutrient- and disease-exposed from samples collected at Mote Marine Laboratory in situ nursery from June to July 2022 Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact http://lod.bco-dmo.org/id/dataset-parameter/1007538.rdf Name: rnaseq_name Units: unitless Description: <p>description needed</p> http://lod.bco-dmo.org/id/dataset-parameter/1007539.rdf Name: sample_name Units: unitless Description: <p>description needed</p> http://lod.bco-dmo.org/id/dataset-parameter/1007540.rdf Name: sample_title Units: unitless Description: <p>description needed</p> http://lod.bco-dmo.org/id/dataset-parameter/1007541.rdf Name: BioSample Units: unitless Description: <p>SRA sample identifier, NCBI Biosample accession ID</p> http://lod.bco-dmo.org/id/dataset-parameter/1007542.rdf Name: BioProject Units: unitless Description: <p>NCBI Bioproject accession ID</p> http://lod.bco-dmo.org/id/dataset-parameter/1007543.rdf Name: organism Units: unitless Description: <p>SRA organism identifier</p> http://lod.bco-dmo.org/id/dataset-parameter/1007544.rdf Name: tissue Units: unitless Description: <p>Tissue of sample</p> http://lod.bco-dmo.org/id/dataset-parameter/1007545.rdf Name: isolation_source Units: unitless Description: <p>Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived.</p> http://lod.bco-dmo.org/id/dataset-parameter/1007546.rdf Name: geo_loc_name Units: unitless Description: <p>sampling location, geographic location of the origin of the sample</p> http://lod.bco-dmo.org/id/dataset-parameter/1007547.rdf Name: lat Units: decimal degrees Description: <p>Latitude of sampling location, south is negative</p> http://lod.bco-dmo.org/id/dataset-parameter/1007549.rdf Name: lon Units: decimal degrees Description: <p>Longitude of sampling location, west is negative</p> http://lod.bco-dmo.org/id/dataset-parameter/1007551.rdf Name: collection_date Units: unitless Description: <p>Collection date of organism</p> http://lod.bco-dmo.org/id/dataset-parameter/1007552.rdf Name: isolate Units: unitless Description: <p>description needed</p> http://lod.bco-dmo.org/id/dataset-parameter/1007553.rdf Name: Genotype Units: unitless Description: <p>Observed genotype</p> http://lod.bco-dmo.org/id/dataset-parameter/1007554.rdf Name: Treatment Units: unitless Description: <p>Treatment protocol</p> http://lod.bco-dmo.org/id/dataset-parameter/1007555.rdf Name: Exposure Units: unitless Description: <p>brief description of exposure to disease of Reef, Nutrients or Baseline</p> http://lod.bco-dmo.org/id/dataset-parameter/1007556.rdf Name: Disease_exposure Units: unitless Description: <p>Disease exposure flag. Can be Unexposed = not exposed to disease, Pre-Exposure = before exposed to disease, Disease Exposed = exposed to disease,</p> http://lod.bco-dmo.org/id/dataset-parameter/1007557.rdf Name: Health_status Units: unitless Description: <p>Health status of sample at time of collection. Can be Baseline, Unexposed= unexposed to disease, Pre-Exposure = before disease exposure, Disease Exposed = exposed to disease,</p> http://lod.bco-dmo.org/id/dataset-parameter/1007558.rdf Name: group Units: unitless Description: <p>Group designation combined from genotype, treatment initial, and disease exposure</p> http://lod.bco-dmo.org/id/dataset-parameter/1007559.rdf Name: title Units: unitless Description: <p>Library title</p> http://lod.bco-dmo.org/id/dataset-parameter/1007560.rdf Name: design_description Units: unitless Description: <p>Description explaining how this library was prepared and sequenced</p> http://lod.bco-dmo.org/id/dataset-parameter/1007561.rdf Name: platform Units: unitless Description: <p>Sequencing platform manufacturer</p> http://lod.bco-dmo.org/id/dataset-parameter/1007562.rdf Name: instrument_model Units: unitless Description: <p>Sequencer model</p> http://lod.bco-dmo.org/id/dataset-parameter/1007563.rdf Name: library_name Units: unitless Description: <p>Unique identifier for the sequencing library (can be the sample name repeated).</p> http://lod.bco-dmo.org/id/dataset-parameter/1007564.rdf Name: library_strategy Units: unitless Description: <p>Sequencing library strategy</p> http://lod.bco-dmo.org/id/dataset-parameter/1007565.rdf Name: library_source Units: unitless Description: <p>Source of sequencing library</p> http://lod.bco-dmo.org/id/dataset-parameter/1007566.rdf Name: library_selection Units: unitless Description: <p>Selection used for sequencing library</p> http://lod.bco-dmo.org/id/dataset-parameter/1007567.rdf Name: library_layout Units: unitless Description: <p>single or paired end sequencing reads</p> http://lod.bco-dmo.org/id/dataset-parameter/1007568.rdf Name: filetype Units: unitless Description: <p>File type</p> http://lod.bco-dmo.org/id/dataset-parameter/1007569.rdf Name: filename Units: unitless Description: <p>Forward reads file name</p> http://lod.bco-dmo.org/id/dataset-parameter/1007570.rdf Name: filename2 Units: unitless Description: <p>Reverse reads file name</p> GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact https://doi.org/10.26008/1912/bco-dmo.924760.1 download onLine dataset &lt;p&gt;Samples of coral tissue, skeleton, and mucus were taken from two genotypes of &lt;em&gt;Acropora cervicornis&lt;/em&gt; prior to nutrient enrichment (n = 20 per genotype), prior to disease exposure (n = 18 per genotype), and at various stages during disease development. The samples&amp;nbsp;were collected at the Mote Marine Laboratory in situ nursery from June to July 2022. All surviving ramets at one week after disease exposure were sampled. To sample each coral, 6-8 polyps were excised using a flame-sterilized blade and placed in a 1.5mL microcentrifuge tube containing 1mL of DNA/RNA shield (Zymo Research, R1100-250, Irvine, CA, USA). Samples were transferred to a -80℃ freezer for long-term storage. In preparation for RNA extractions, the samples were removed from the -80℃ freezer and thawed on ice. With flame-sterilized tweezers, half of the biomass was transferred to a Disruptor Tube (Omega Bio-Tek, Norcross, GA, USA), the other half was kept as a bioarchive and returned to -80℃. RNA from each sample was isolated utilizing the E.Z.N.A. DNA/RNA Isolation Kit (Omega Bio-Tek, Norcross, GA, USA) with slight modifications to the manufacturer’s protocol to increase yield. RNA isolates were stored at -80℃. DNA quantity and quality was assessed utilizing a NanoDrop spectrophotometer (Thermo Fisher Scientific™, Waltham, MA, USA). Samples were shipped on dry ice to the&amp;nbsp;Oklahoma Medical Research Foundation NGS Core, where RNA cleanup, precipitation, and polyA selection was performed.&amp;nbsp; Libraries were prepared using the IDT xGen RNA Library kit. Final QC was performed using KAPA qPCR and Agilent Tapestation to confirm rRNA content, and libraries were sequenced on a NovaSeq 6000 using S4 chemistry.&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;A total of 42 samples were successfully sequenced on an Illumina NovaSeq 6000 with S4 chemistry and PE 150 bp reads. Prior to quality filtering, an average single-end read depth of 11,084,445.3 +/-&amp;nbsp; 970,330.08 was produced from sequencing. After filtration, an average of 10,954,237.2 +/- 982,482.11 reads remained per read direction. From quality filtered sequences, 72.54% of single end reads mapped to the &lt;em&gt;A. cervicornis&lt;/em&gt; transcriptome using STAR. Quantification using Salmon resulted in 24,875 genes having at least one count across all samples, with subsequent filtering (less than 1 count in &amp;gt;10 samples) reducing this to 12,913 genes for downstream analysis. Of reads not aligning to the &lt;em&gt;A. cervicornis&lt;/em&gt; transcriptome, an average of 22.54% aligned to the Symbiodinium (Clade A) reference transcriptome using STAR. Quantification using Salmon yielded counts for 73,112 transcripts, with 26,225 of these retained for downstream analysis after filtering (less than 1 count in greater than 10 samples). Analysis of differentially expressed transcripts is ongoing.&lt;/p&gt; Specified by the Principal Investigator(s) This section documents curation actions performed prior to publication review with the submitter, and additional information relevant to understanding and reusing this dataset. It distinguishes changes made to the submitted (meta)data from unresolved issues and/or enhancements that improve future reuse and interoperability. CURATION ACTIONS PERFORMED ON DATA - Imported all tables, treating &quot;&quot; and nd as missing values. - Merged all tables, removing duplicate columns. Joins based on sample name and sample identifier, creating a summary table of NCBI files - One value was corrected to permit matching: the derived identifier in row 33 carried a trailing 'A' (46-N13-DT1A) not present in the sample title at NCBI, and was corrected to 46-N13-DT1. Published library_name for row 33 still carries the 'A' while sample_title does not. - Removed empty, constant-valued, and redundant file-pointer columns - &quot;collection_date&quot; was converted from mm-dd-yy to ISO 8601 (yyyy-mm-dd). - Constant columns were added by BCO-DMO: lat (24.56257) and lon (-81.40009), the nominal Mote Marine Laboratory collection location, and BioProject (PRJNA1047741) - Replaced special characters, spaces and periods from parameter names with underscores CURATION ACTIONS PERFORMED ON METADATA - BCO-DMO's standard metadata entry and text formatting steps were performed. See: https://www.bco-dmo.org/how-to/standard-curation-edits - NCBI BioProject PRJNA1047741 was recorded as a related resource ISSUES POTENTIALLY IMPACTING REUSE - The submitted text used 'Aquarickettsia rohweri'. Proposed to change this to 'Candidatus Aquarickettsia rohweri' to match NCBI Taxonomy (taxid 2602574), under which the dataset's sequence accessions are registered. - Parameter descriptions were not supplied. Inferred descriptions for all parameters where possible. Specified by BCO-DMO Data Managers asNeeded 7.x-1.1 Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact Illumina Nova Seq 6000 Illumina Nova Seq 6000 PI Supplied Instrument Name: Illumina Nova Seq 6000 Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. PI Supplied Instrument Name: Instrument Name: Thermo Scientific NanoDrop spectrophotometer Instrument Short Name:NanoDrop spectrophotometer Instrument Description: Thermo Scientific NanoDrop spectrophotometers provide microvolume quantification and purity assessments of DNA, RNA, and protein samples. NanoDrop spectrophotometers work on the principle of ultraviolet-visible spectrum (UV-Vis) absorbance. The range consists of the NanoDrop One/OneC UV-Vis Spectrophotometers, NanoDrop Eight UV-Vis Spectrophotometer and NanoDrop Lite Plus UV Spectrophotometer.