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Title Sum-
Institution Dataset ID
   set  data        files  public Eastern oyster gonad methylation patterns in response to experimental ocean acidification    ?     I   M   background (external link) RSS Subscribe BCO-DMO bcodmo_dataset_785167

The Dataset's Variables and Attributes

Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv
attribute NC_GLOBAL acquisition_description String Adult C. virginica (9.55 cm \u00b1 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 \u00b5atm) or elevated pCO2 (2500 \u00b5atm; \u03a9calcite < 1).

DNA was isolated from ten gonad tissue samples using the E.Z.N.A. Mollusc Kit
(Omega) according to the manufacturer\u2019s instructions. Isolated DNA was
quantified using a Qubit dsDNA BR Kit (Invitrogen). DNA samples were sonicated
for ten minutes at 4 \u00baC, 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).
attribute NC_GLOBAL awards_0_award_nid String 666497
attribute NC_GLOBAL awards_0_award_number String OCE-1635423
attribute NC_GLOBAL awards_0_data_url String https://www.nsf.gov/awardsearch/showAward?AWD_ID=1635423 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String Daniel Thornhill
attribute NC_GLOBAL awards_0_program_manager_nid String 722161
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Crassostrea virginica gonad MBD-BSseq at high pCO2
Metadata for GenBank BioProject PRJNA513384
Collected at Plum Island Sound, MA (42.681764, -70.813498), July 2016

PI's: K. Lotterhos, J. Ries (NEU), S. Roberts (UW)
version date: 2019-12-30
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3 19 Dec 2019
attribute NC_GLOBAL date_created String 2019-12-30T19:14:16Z
attribute NC_GLOBAL date_modified String 2020-01-13T16:34:23Z
attribute NC_GLOBAL defaultDataQuery String &amp;time&lt;now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.785167.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/785167 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Automated Sequencer
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Paired-end 100bp DNA sequencing was performed on the Illumina HiSeq1500 system.
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 785193
attribute NC_GLOBAL instruments_0_description String General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.
attribute NC_GLOBAL instruments_0_instrument_name String Automated DNA Sequencer
attribute NC_GLOBAL instruments_0_instrument_nid String 649
attribute NC_GLOBAL instruments_0_supplied_name String Illumina HiSeq1500
attribute NC_GLOBAL keywords String accession, bco, bco-dmo, biological, bioproject, bioproject_accession, biosample, biosample_accession, carbon, carbon dioxide, chemical, co2, data, dataset, description, design, design_description, dioxide, dmo, erddap, filename, filename2, filetype, instrument, instrument_model, layout, library, library_ID, library_layout, library_selection, library_source, library_strategy, management, mbd, MBD_cv_id, model, oceanography, office, pCO2_treatment, platform, preliminary, selection, source, strategy, title, treatment
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/785167/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/785167 (external link)
attribute NC_GLOBAL param_mapping String {'785167': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/785167/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Northeastern University
attribute NC_GLOBAL people_0_affiliation_acronym String NEU
attribute NC_GLOBAL people_0_person_name String Kathleen Lotterhos
attribute NC_GLOBAL people_0_person_nid String 666501
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String Northeastern University
attribute NC_GLOBAL people_1_affiliation_acronym String NEU
attribute NC_GLOBAL people_1_person_name String Justin B. Ries
attribute NC_GLOBAL people_1_person_nid String 51345
attribute NC_GLOBAL people_1_role String Co-Principal Investigator
attribute NC_GLOBAL people_1_role_type String originator
attribute NC_GLOBAL people_2_affiliation String University of Washington
attribute NC_GLOBAL people_2_affiliation_acronym String UW
attribute NC_GLOBAL people_2_person_name String Steven Roberts
attribute NC_GLOBAL people_2_person_nid String 666500
attribute NC_GLOBAL people_2_role String Co-Principal Investigator
attribute NC_GLOBAL people_2_role_type String originator
attribute NC_GLOBAL people_3_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_3_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_3_person_name String Nancy Copley
attribute NC_GLOBAL people_3_person_nid String 50396
attribute NC_GLOBAL people_3_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_3_role_type String related
attribute NC_GLOBAL project String Epigenetics to Ocean
attribute NC_GLOBAL projects_0_acronym String Epigenetics to Ocean
attribute NC_GLOBAL projects_0_description String NSF Award Abstract:
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.
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.
attribute NC_GLOBAL projects_0_end_date String 2019-12
attribute NC_GLOBAL projects_0_geolocation String Coastal Massachusetts near Nahant: 42°25'06"N 70°54'14"W
attribute NC_GLOBAL projects_0_name String Collaborative Research: Does ocean acidification induce a methylation response that affects the fitness of the next generation in oysters?
attribute NC_GLOBAL projects_0_project_nid String 666496
attribute NC_GLOBAL projects_0_start_date String 2017-01
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String bioproject_accession,title,library_strategy,library_source,library_selection,library_layout,platform,instrument_model,filetype
attribute NC_GLOBAL summary String 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.
attribute NC_GLOBAL title String Eastern oyster gonad methylation patterns in response to experimental ocean acidification
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable bioproject_accession   String  
attribute bioproject_accession bcodmo_name String accession number
attribute bioproject_accession description String GenBank BioProject accession identifier
attribute bioproject_accession long_name String Bioproject Accession
attribute bioproject_accession units String unitless
variable biosample_accession   String  
attribute biosample_accession bcodmo_name String accession number
attribute biosample_accession description String GenBank BioSample accession identifier
attribute biosample_accession long_name String Biosample Accession
attribute biosample_accession units String unitless
variable library_ID   String  
attribute library_ID bcodmo_name String sample
attribute library_ID description String sample identifier used in library preparation
attribute library_ID long_name String Library ID
attribute library_ID nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute library_ID units String unitless
variable title   String  
attribute title bcodmo_name String sample_descrip
attribute title description String GenBank BioProject title
attribute title long_name String Title
attribute title units String unitless
variable library_strategy   String  
attribute library_strategy bcodmo_name String sample_descrip
attribute library_strategy description String strategy used for sequencing: MBD-Seq = Direct sequencing of methylated fractions sequencing strategy
attribute library_strategy long_name String Library Strategy
attribute library_strategy units String unitless
variable library_source   String  
attribute library_source bcodmo_name String sample_descrip
attribute library_source description String source material (genomic DNA)
attribute library_source long_name String Library Source
attribute library_source units String unitless
variable library_selection   String  
attribute library_selection bcodmo_name String sample_descrip
attribute library_selection description String Method by which the material was selected: MBD2 protein methyl-CpG binding domain
attribute library_selection long_name String Library Selection
attribute library_selection units String unitless
variable library_layout   String  
attribute library_layout bcodmo_name String sample_descrip
attribute library_layout description String either a paired-end or single sequence run
attribute library_layout long_name String Library Layout
attribute library_layout units String unitless
variable platform   String  
attribute platform bcodmo_name String instrument
attribute platform description String instrument type used to sequence DNA
attribute platform long_name String Platform
attribute platform units String unitless
variable instrument_model   String  
attribute instrument_model bcodmo_name String inst_model
attribute instrument_model description String DNA sequencing insturment model
attribute instrument_model long_name String Instrument Model
attribute instrument_model units String unitless
variable design_description   String  
attribute design_description bcodmo_name String sample_descrip
attribute design_description description String method detail used in sequencing: whether run in Lane 1 or Lane 2
attribute design_description long_name String Design Description
attribute design_description units String unitless
variable filetype   String  
attribute filetype bcodmo_name String unknown
attribute filetype description String type of genomics file (fastq)
attribute filetype long_name String Filetype
attribute filetype units String unitless
variable filename   String  
attribute filename bcodmo_name String file_name
attribute filename description String filename of first paired-end sequencing file
attribute filename long_name String Filename
attribute filename units String unitless
variable filename2   String  
attribute filename2 bcodmo_name String file_name
attribute filename2 description String filename of second paired-end sequencing file
attribute filename2 long_name String Filename2
attribute filename2 units String unitless
variable MBD_cv_id   String  
attribute MBD_cv_id bcodmo_name String sample
attribute MBD_cv_id description String MBD Cv identifier
attribute MBD_cv_id long_name String MBD Cv Id
attribute MBD_cv_id nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute MBD_cv_id units String unitless
variable pCO2_treatment   String  
attribute pCO2_treatment bcodmo_name String pCO2
attribute pCO2_treatment description String pCO2 treatment
attribute pCO2_treatment long_name String P CO2 Treatment
attribute pCO2_treatment nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/PCO2C101/ (external link)
attribute pCO2_treatment units String ppm

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.

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