ERDDAP > info > bcodmo_dataset_785167

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	FGDC, ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
	set	data			files	public	[Crassostrea virginica gonad MBD-BSseq] - Eastern oyster gonad methylation patterns in response to experimental ocean acidification (Collaborative Research: Does ocean acidification induce a methylation response that affects the fitness of the next generation in oysters?)		I   M	background			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
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/
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
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
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/785167
attribute	NC_GLOBAL	param_mapping	String	{'785167': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/785167/parameters
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	[Crassostrea virginica gonad MBD-BSseq] - Eastern oyster gonad methylation patterns in response to experimental ocean acidification (Collaborative Research: Does ocean acidification induce a methylation response that affects the fitness of the next generation in oysters?)
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/
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/
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/
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.