Dataset: Crassostrea virginica gonad MBD-BSseq

Name: Eastern oyster gonad methylation patterns in response to experimental ocean acidification
Published: 2019-12-30
Keywords: Eastern oyster, epigenetics, gonad tissue, MBD-BSSeq, biota, oceans

Cite This Dataset

DOI:10.1575/1912/bco-dmo.785167.1

Spatial Extent: N:42.681764 E:-70.813498 S:42.681764 W:-70.813498

Temporal Extent: 2016-07 - 2016-07

Project:

Collaborative Research: Does ocean acidification induce a methylation response that affects the fitness of the next generation in oysters? (Epigenetics to Ocean)

Principal Investigator:

Katie Lotterhos (Northeastern University)

Co-Principal Investigator:

Justin B. Ries (Northeastern University)

Steven Roberts (University of Washington, UW)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2019-12-30

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Eastern oyster gonad methylation patterns in response to experimental ocean acidification

Abstract:

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.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2019-12-30	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.1575/1912/bco-dmo.785167.1	2020-01-13

Description

Methods & Sampling

Adult C. virginica (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 pCO₂ (2500 µatm; Ω_calcite < 1).

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).

Data Processing Description

BCO-DMO Processing Notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names: filename3 to MBD_cv_id; filename4 to pCO2_treatment

Data Files

File
oyster_sra.csv (Comma Separated Values (.csv), 2.79 KB) MD5:7f69862f69eb1f776c2b67b102d69ea4 Primary data file for dataset ID 785167

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1635423

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: Illumina HiSeq1500

Supplied Description:

Paired-end 100bp DNA sequencing was performed on the Illumina HiSeq1500 system.

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic 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.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
bioproject_accession	GenBank BioProject accession identifier	unitless	accession_number
biosample_accession	GenBank BioSample accession identifier	unitless	accession_number
library_ID	sample identifier used in library preparation	unitless	sample
title	GenBank BioProject title	unitless	sample_descrip
library_strategy	strategy used for sequencing: MBD-Seq = Direct sequencing of methylated fractions sequencing strategy	unitless	sample_descrip
library_source	source material (genomic DNA)	unitless	sample_descrip
library_selection	Method by which the material was selected: MBD2 protein methyl-CpG binding domain	unitless	sample_descrip
library_layout	either a paired-end or single sequence run	unitless	sample_descrip
platform	instrument type used to sequence DNA	unitless	instrument
instrument_model	DNA sequencing insturment model	unitless	inst_model
design_description	method detail used in sequencing: whether run in Lane 1 or Lane 2	unitless	sample_descrip
filetype	type of genomics file (fastq)	unitless	no_bcodmo_term
filename	filename of first paired-end sequencing file	unitless	file_name
filename2	filename of second paired-end sequencing file	unitless	file_name
MBD_cv_id	MBD Cv identifier	unitless	sample
pCO2_treatment	pCO2 treatment	ppm	pCO2