http://lod.bco-dmo.org/id/dataset/785167 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 2019-12-30 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Eastern oyster gonad methylation patterns in response to experimental ocean acidification 2019-12-30 publication 2019-12-30 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2020-01-13 publication https://doi.org/10.1575/1912/bco-dmo.785167.1 Katie Lotterhos Northeastern University principalInvestigator Justin B. Ries Northeastern University principalInvestigator Steven Roberts University of Washington 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: Lotterhos, K., Ries, J., Roberts, S. (2019) Eastern oyster gonad methylation patterns in response to experimental ocean acidification. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2019-12-30 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.785167.1 [access date] GenBank metadata for Eastern oyster gonad methylation and OA Dataset Description: &lt;p&gt;Eastern oyster gonad methylation patterns in response to experimental ocean acidification at pCO2 levels 400 and 2800 ppm. Oysters were collected from an intertidal oyster reef in Plum Island Sound, MA, Gulf of Maine in mid-July 2016. This dataset includes GenBank BioProject PRJNA513384 metadata.&lt;/p&gt; Methods and Sampling: &lt;p&gt;Adult &lt;em&gt;C. virginica&lt;/em&gt; (9.55 cm ± 0.45) were collected from an intertidal oyster reef in Plum Island Sound, MA (42.681764, -70.813498) in mid-July 2016. The oysters were transported to the Marine Science Center at Northeastern University (Nahant, MA), where they were cleaned and randomly assigned to one of six flow-through tanks (50L) maintained at ambient seawater conditions. Oysters were acclimated for 14 days under ambient conditions, before initiating a 28-day experimental exposure. The oysters were exposed to either control (500 µatm) or elevated pCO&lt;sub&gt;2&lt;/sub&gt; (2500 µatm; Ω&lt;sub&gt;calcite&lt;/sub&gt; &amp;lt; 1).&lt;/p&gt; &lt;p&gt;DNA was isolated from ten gonad tissue samples using the E.Z.N.A. Mollusc Kit (Omega) according to the manufacturer’s instructions. Isolated DNA was quantified using a Qubit dsDNA BR Kit (Invitrogen). DNA samples were sonicated for ten minutes at 4 ºC, on 30 second intervals periods at 25% intensity. Shearing size (350bp) was verified using a 2200 TapeStation System (Agilent Technologies). Samples (10) were enriched for methylated DNA using MethylMiner kit (Invitrogen). Libraries were prepared using Pico Methyl-Seq Library Prep Kit (Cat. #D5455).&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1635423 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1635423 completed Katie Lotterhos Northeastern University 781-581-7370 X304 Northeastern University Marine Sciences Center 430 Nahant Rd. Nahant MA 01908 USA k.lotterhos@northeastern.edu pointOfContact Justin B. Ries Northeastern University 781-581-7370 Northeastern University Marine Science Center 430 Nahant Rd. Nahant MA 01908 USA j.ries@northeastern.edu pointOfContact Steven Roberts University of Washington 208-866-5141 1140 NE Boat Street Fisheries Research and Teaching Building; Rm 232 Seattle WA 98105 sr320@uw.edu pointOfContact asNeeded Dataset Version: 1 Unknown bioproject_accession biosample_accession library_ID title library_strategy library_source library_selection library_layout platform instrument_model design_description filetype filename filename2 MBD_cv_id pCO2_treatment Illumina HiSeq1500 theme None, User defined accession number sample identification sample description instrument instrument model No BCO-DMO term file_name Partial pressure of CO2 featureType BCO-DMO Standard Parameters Automated DNA Sequencer 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: Does ocean acidification induce a methylation response that affects the fitness of the next generation in oysters? https://osprey.bco-dmo.org/project/666496 Collaborative Research: Does ocean acidification induce a methylation response that affects the fitness of the next generation in oysters? <p><em>NSF Award Abstract:</em><br /> Marine ecosystems worldwide are threatened by ocean acidification, a process caused by the unprecedented rate at which carbon dioxide is increasing in the atmosphere. Since ocean change is predicted to be rapid, extreme, and widespread, marine species may face an "adapt-or-die" scenario. However, modifications to the DNA sequence may be induced in response to a stress like ocean acidification and then inherited. Such "epigenetic" modifications may hold the key to population viability under global climate change, but they have been understudied. The aim of this research is to characterize the role of DNA methylation, a heritable epigenetic system, in the response of Eastern oysters (Crassostrea virginica) to ocean acidification. The intellectual merit lies in the integrative approach, which will characterize the role of DNA methylation in the intergenerational response of oysters to ocean acidification. These interdisciplinary data, spanning from molecular to organismal levels, will provide insight into mechanisms that underlie the capacity of marine invertebrates to respond to ocean acidification and lay the foundation for future transgenerational studies. Ocean acidification currently threatens marine species worldwide and has already caused significant losses in aquaculture, especially in Crassostrea species. This research has broader impacts for breeding, aquaculture, and the economy. Under the investigators' "Epigenetics to Ocean" (E2O) training program, the investigators will build STEM talent in bioinformatics and biogeochemistry, expose girls in low-income school districts to careers in genomics, and advance the field through open science and reproducibility.</p> <p>This research will specifically test if intermittent exposure to low pH induces a methylation response with downstream beneficial effects for biomineralization. These methylation states could be inherited and confer a fitness advantage to larvae that possess them. Phase 1 of the project will use an exposure experiment to determine the degree to which DNA methylation is altered and regulates the response to OA. Data from this experiment will be used to test the hypotheses that (i) DNA methylation, induced in the tissue of shell formation (i.e., mantle tissue), is correlated with changes in transcription and regulation of pallial fluid pH (calcifying fluid pH, measured by microelectrode), and (ii) that methylation changes induced in the mantle tissue are also induced in the germline --indicating that such changes are potentially heritable. Phase 2 of the project will use a pair-mated cross experiment to test the hypothesis that parental exposure to OA alters larval traits (calcification rate, shell structure, and polymorph mineralogy). Larvae will be generated from parents exposed to OA or control seawater, and then raised under control or OA conditions. Results will be used to (i) characterize inheritance of induced methylation states, (ii) estimate the variance in larval traits explained by genotype, non-genetic maternal/paternal effects, adult OA exposure, larval OA exposure, and parental methylome, and (iii) test the hypothesis that adult exposure alters the heritability (a quantity that predicts evolutionary response) of larval traits. Since the effects of epigenetic phenomena on estimates of heritability are highly debated, the results would advance understanding of this important issue. Because the investigators could discover that DNA methylation is a mechanism for heritable plastic responses to OA, knowledge of this mechanism would significantly improve and potentially transform predictive models for how organisms respond to global change.</p> Epigenetics to Ocean largerWorkCitation project eng; USA biota oceans -70.813498 -70.813498 42.681764 42.681764 2016-07-01 2016-07-31 Coastal Massachusetts near Nahant: 42°25&#039;06&quot;N 70°54&#039;14&quot;W 0 BCO-DMO catalogue of parameters from Eastern oyster gonad methylation patterns in response to experimental ocean acidification 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/787216.rdf Name: bioproject_accession Units: unitless Description: <p>GenBank BioProject accession identifier</p> http://lod.bco-dmo.org/id/dataset-parameter/787217.rdf Name: biosample_accession Units: unitless Description: <p>GenBank BioSample accession identifier</p> http://lod.bco-dmo.org/id/dataset-parameter/787218.rdf Name: library_ID Units: unitless Description: <p>sample identifier used in library preparation</p> http://lod.bco-dmo.org/id/dataset-parameter/787219.rdf Name: title Units: unitless Description: <p>GenBank BioProject title</p> http://lod.bco-dmo.org/id/dataset-parameter/787220.rdf Name: library_strategy Units: unitless Description: <p>strategy used for sequencing: MBD-Seq = Direct sequencing of methylated fractions sequencing strategy</p> http://lod.bco-dmo.org/id/dataset-parameter/787221.rdf Name: library_source Units: unitless Description: <p>source material (genomic DNA)</p> http://lod.bco-dmo.org/id/dataset-parameter/787222.rdf Name: library_selection Units: unitless Description: <p>Method by which the material was selected: MBD2 protein methyl-CpG binding domain</p> http://lod.bco-dmo.org/id/dataset-parameter/787223.rdf Name: library_layout Units: unitless Description: <p>either a paired-end or single sequence run</p> http://lod.bco-dmo.org/id/dataset-parameter/787224.rdf Name: platform Units: unitless Description: <p>instrument type used to sequence DNA</p> http://lod.bco-dmo.org/id/dataset-parameter/787225.rdf Name: instrument_model Units: unitless Description: <p>DNA sequencing insturment model</p> http://lod.bco-dmo.org/id/dataset-parameter/787226.rdf Name: design_description Units: unitless Description: <p>method detail used in sequencing: whether run in Lane 1 or Lane 2</p> http://lod.bco-dmo.org/id/dataset-parameter/787227.rdf Name: filetype Units: unitless Description: <p>type of genomics file (fastq)</p> http://lod.bco-dmo.org/id/dataset-parameter/787228.rdf Name: filename Units: unitless Description: <p>filename of first paired-end sequencing file</p> http://lod.bco-dmo.org/id/dataset-parameter/787229.rdf Name: filename2 Units: unitless Description: <p>filename of second paired-end sequencing file</p> http://lod.bco-dmo.org/id/dataset-parameter/787230.rdf Name: MBD_cv_id Units: unitless Description: <p>MBD Cv identifier</p> http://lod.bco-dmo.org/id/dataset-parameter/787231.rdf Name: pCO2_treatment Units: ppm Description: <p>pCO2 treatment</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 2854 https://darchive.mblwhoilibrary.org/bitstream/1912/25138/1/dataset-785167_crassostrea-virginica-gonad-mbd-bsseq__v1.tsv download https://doi.org/10.1575/1912/bco-dmo.785167.1 download onLine dataset &lt;p&gt;Adult &lt;em&gt;C. virginica&lt;/em&gt; (9.55 cm ± 0.45) were collected from an intertidal oyster reef in Plum Island Sound, MA (42.681764, -70.813498) in mid-July 2016. The oysters were transported to the Marine Science Center at Northeastern University (Nahant, MA), where they were cleaned and randomly assigned to one of six flow-through tanks (50L) maintained at ambient seawater conditions. Oysters were acclimated for 14 days under ambient conditions, before initiating a 28-day experimental exposure. The oysters were exposed to either control (500 µatm) or elevated pCO&lt;sub&gt;2&lt;/sub&gt; (2500 µatm; Ω&lt;sub&gt;calcite&lt;/sub&gt; &amp;lt; 1).&lt;/p&gt; &lt;p&gt;DNA was isolated from ten gonad tissue samples using the E.Z.N.A. Mollusc Kit (Omega) according to the manufacturer’s instructions. Isolated DNA was quantified using a Qubit dsDNA BR Kit (Invitrogen). DNA samples were sonicated for ten minutes at 4 ºC, on 30 second intervals periods at 25% intensity. Shearing size (350bp) was verified using a 2200 TapeStation System (Agilent Technologies). Samples (10) were enriched for methylated DNA using MethylMiner kit (Invitrogen). Libraries were prepared using Pico Methyl-Seq Library Prep Kit (Cat. #D5455).&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;&lt;strong&gt;BCO-DMO Processing Notes:&lt;/strong&gt;&lt;br /&gt; - added conventional header with dataset name, PI name, version date&lt;br /&gt; - modified parameter names: filename3 to MBD_cv_id; filename4 to pCO2_treatment&lt;/p&gt; &lt;p&gt;&amp;nbsp;&lt;/p&gt; Specified by the Principal Investigator(s) 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 HiSeq1500 Illumina HiSeq1500 PI Supplied Instrument Name: Illumina HiSeq1500 PI Supplied Instrument Description:Paired-end 100bp DNA sequencing was performed on the Illumina HiSeq1500 system. 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.