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Dataset Title:  Eastern oyster gonad methylation patterns in response to experimental ocean
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_785167)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Subset | Files
Variable ?   Optional
Constraint #1 ?
Constraint #2 ?
   Minimum ?
   or a List of Values ?
   Maximum ?
 bioproject_accession (unitless) ?      
   - +  ?
 biosample_accession (unitless) ?          "SAMN10712180"    "SAMN10715985"
 library_ID (unitless) ?          "zr2096_10_s1"    "zr2096_9_s1"
 title (unitless) ?      
   - +  ?
 library_strategy (unitless) ?      
   - +  ?
 library_source (unitless) ?      
   - +  ?
 library_selection (unitless) ?      
   - +  ?
 library_layout (unitless) ?      
   - +  ?
 platform (unitless) ?      
   - +  ?
 instrument_model (unitless) ?      
   - +  ?
 design_description (unitless) ?          "Run in Lane 1"    "Run in Lane 2"
 filetype (unitless) ?      
   - +  ?
 filename (unitless) ?          "zr2096_10_s1_R1_va..."    "zr2096_9_s1_R1_val..."
 filename2 (unitless) ?          "zr2096_10_s1_R2_va..."    "zr2096_9_s1_R2_val..."
 MBD_cv_id (unitless) ?          "MBD Cv 103"    "MBD Cv 36"
 pCO2_treatment (ppm) ?          "2800 ppm"    "400 ppm"
Server-side Functions ?
 distinct() ?
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File type: (more info)

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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  bioproject_accession {
    String bcodmo_name "accession number";
    String description "GenBank BioProject accession identifier";
    String long_name "Bioproject Accession";
    String units "unitless";
  biosample_accession {
    String bcodmo_name "accession number";
    String description "GenBank BioSample accession identifier";
    String long_name "Biosample Accession";
    String units "unitless";
  library_ID {
    String bcodmo_name "sample";
    String description "sample identifier used in library preparation";
    String long_name "Library ID";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
  title {
    String bcodmo_name "sample_descrip";
    String description "GenBank BioProject title";
    String long_name "Title";
    String units "unitless";
  library_strategy {
    String bcodmo_name "sample_descrip";
    String description "strategy used for sequencing: MBD-Seq = Direct sequencing of methylated fractions sequencing strategy";
    String long_name "Library Strategy";
    String units "unitless";
  library_source {
    String bcodmo_name "sample_descrip";
    String description "source material (genomic DNA)";
    String long_name "Library Source";
    String units "unitless";
  library_selection {
    String bcodmo_name "sample_descrip";
    String description "Method by which the material was selected: MBD2 protein methyl-CpG binding domain";
    String long_name "Library Selection";
    String units "unitless";
  library_layout {
    String bcodmo_name "sample_descrip";
    String description "either a paired-end or single sequence run";
    String long_name "Library Layout";
    String units "unitless";
  platform {
    String bcodmo_name "instrument";
    String description "instrument type used to sequence DNA";
    String long_name "Platform";
    String units "unitless";
  instrument_model {
    String bcodmo_name "inst_model";
    String description "DNA sequencing insturment model";
    String long_name "Instrument Model";
    String units "unitless";
  design_description {
    String bcodmo_name "sample_descrip";
    String description "method detail used in sequencing: whether run in Lane 1 or Lane 2";
    String long_name "Design Description";
    String units "unitless";
  filetype {
    String bcodmo_name "unknown";
    String description "type of genomics file (fastq)";
    String long_name "Filetype";
    String units "unitless";
  filename {
    String bcodmo_name "file_name";
    String description "filename of first paired-end sequencing file";
    String long_name "Filename";
    String units "unitless";
  filename2 {
    String bcodmo_name "file_name";
    String description "filename of second paired-end sequencing file";
    String long_name "Filename2";
    String units "unitless";
  MBD_cv_id {
    String bcodmo_name "sample";
    String description "MBD Cv identifier";
    String long_name "MBD Cv Id";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
  pCO2_treatment {
    String bcodmo_name "pCO2";
    String description "pCO2 treatment";
    String long_name "P CO2 Treatment";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PCO2C101/";
    String units "ppm";
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"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).";
    String awards_0_award_nid "666497";
    String awards_0_award_number "OCE-1635423";
    String awards_0_data_url "https://www.nsf.gov/awardsearch/showAward?AWD_ID=1635423";
    String awards_0_funder_name "NSF Division of Ocean Sciences";
    String awards_0_funding_acronym "NSF OCE";
    String awards_0_funding_source_nid "355";
    String awards_0_program_manager "Daniel Thornhill";
    String awards_0_program_manager_nid "722161";
    String cdm_data_type "Other";
    String comment 
"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";
    String Conventions "COARDS, CF-1.6, ACDD-1.3";
    String creator_email "info@bco-dmo.org";
    String creator_name "BCO-DMO";
    String creator_type "institution";
    String creator_url "https://www.bco-dmo.org/";
    String data_source "extract_data_as_tsv version 2.3  19 Dec 2019";
    String date_created "2019-12-30T19:14:16Z";
    String date_modified "2020-01-13T16:34:23Z";
    String defaultDataQuery "&amp;time&lt;now";
    String doi "10.1575/1912/bco-dmo.785167.1";
    String history 
"2022-08-17T11:10:24Z (local files)
2022-08-17T11:10:24Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_785167.html";
    String infoUrl "https://www.bco-dmo.org/dataset/785167";
    String institution "BCO-DMO";
    String instruments_0_acronym "Automated Sequencer";
    String instruments_0_dataset_instrument_description "Paired-end 100bp DNA sequencing was performed on the Illumina HiSeq1500 system.";
    String instruments_0_dataset_instrument_nid "785193";
    String instruments_0_description "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.";
    String instruments_0_instrument_name "Automated DNA Sequencer";
    String instruments_0_instrument_nid "649";
    String instruments_0_supplied_name "Illumina HiSeq1500";
    String keywords "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";
    String license "https://www.bco-dmo.org/dataset/785167/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/785167";
    String param_mapping "{'785167': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/785167/parameters";
    String people_0_affiliation "Northeastern University";
    String people_0_affiliation_acronym "NEU";
    String people_0_person_name "Kathleen Lotterhos";
    String people_0_person_nid "666501";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Northeastern University";
    String people_1_affiliation_acronym "NEU";
    String people_1_person_name "Justin B. Ries";
    String people_1_person_nid "51345";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String people_2_affiliation "University of Washington";
    String people_2_affiliation_acronym "UW";
    String people_2_person_name "Steven Roberts";
    String people_2_person_nid "666500";
    String people_2_role "Co-Principal Investigator";
    String people_2_role_type "originator";
    String people_3_affiliation "Woods Hole Oceanographic Institution";
    String people_3_affiliation_acronym "WHOI BCO-DMO";
    String people_3_person_name "Nancy Copley";
    String people_3_person_nid "50396";
    String people_3_role "BCO-DMO Data Manager";
    String people_3_role_type "related";
    String project "Epigenetics to Ocean";
    String projects_0_acronym "Epigenetics to Ocean";
    String projects_0_description 
"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.";
    String projects_0_end_date "2019-12";
    String projects_0_geolocation "Coastal Massachusetts near Nahant: 42°25'06\"N   70°54'14\"W";
    String projects_0_name "Collaborative Research: Does ocean acidification induce a methylation response that affects the fitness of the next generation in oysters?";
    String projects_0_project_nid "666496";
    String projects_0_start_date "2017-01";
    String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    String standard_name_vocabulary "CF Standard Name Table v55";
    String subsetVariables "bioproject_accession,title,library_strategy,library_source,library_selection,library_layout,platform,instrument_model,filetype";
    String summary "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.";
    String title "Eastern oyster gonad methylation patterns in response to experimental ocean acidification";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.3";


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