Dataset: Oyster Rocks CpG

Name: Metagenomes from Delaware estuarine riverbank sediments obtained by push corer in July 2012
Published: 2015-12-04
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:38.802161 E:-75.20299 S:38.802161 W:-75.20299

Project:

Metagenomic analysis of microbial CpG methylation in Delaware estuarine riverbank sediment (Microbial CpG Methylation )

Program:

Center for Dark Energy Biosphere Investigations (C-DEBI)

Principal Investigator:

Jennifer F. Biddle (University of Delaware)

Co-Principal Investigator:

Dr Adam Marsh (University of Delaware)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

04 Dec 2015

Version Date:

2015-12-04

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Metagenomes from Delaware estuarine riverbank sediments obtained by push corer in July 2012

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Description

Metagenomes from Delaware estuarine riverbank sediment.

Methods & Sampling

Sample collection and storage: A riverbank sediment core was extracted from the Oyster Rocks site of the Broadkill River in Milton, Delaware in July 2012, accessed on foot. Extraction was performed with a polycarbonate push core. Samples were taken in 3 cm slices along the depth of the core and frozen at -80 degrees C until DNA extractions were performed.

DNA digestion and Illumina sequencing: DNA was extracted using a MoBio Powersoil DNA kit. Extracted DNA was digested with HpaII restriction endonuclease. Illumina library preparation and 150-cycle single-read sequencing was performed on an Illumina Hi-Seq 2500 at the University of Delaware Sequencing and Genotyping Center (Delaware Biotechnology Institute).

Raw reads are publicly available through the European Nucleotide Archive at http://www.ebi.ac.uk/ena/data/view/ERP013107

Data Files

File
OysterRocks_metagenomes.csv (Comma Separated Values (.csv), 212 bytes) MD5:53b329776f88f57a303e1e28d314b803 Primary data file for dataset ID 628253

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-0939564

Deployments

None available yet

Instruments

Push Corer

Supplied Name: polycarbonate push core

Supplied Description:

A riverbank sediment core was extracted from the Oyster Rocks site of the Broadkill River in Milton, Delaware in July 2012. Extraction was performed with a polycarbonate push core.

Instrument Type

Generic Name: Push Corer

Generic Description:

Capable of being performed in numerous environments, push coring is just as it sounds. Push coring is simply pushing the core barrel (often an aluminum or polycarbonate tube) into the sediment by hand. A push core is useful in that it causes very little disturbance to the more delicate upper layers of a sub-aqueous sediment.

Description obtained from: http://web.whoi.edu/coastal-group/about/how-we-work/field-methods/coring/

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
site	Description/name of site.	dimensionless	site
lat	Latitude of sampling site.	decimal degrees	lat
lon	Longitude of sampling site. (Negative = West)	decimal degrees	lon
description	Brief description of the data.	dimensionless	brief_desc
ENA_ID	Project ID number in the European Nucleotide Archive.	dimensionless	accession_number
ENA_URL	Hyperlink to European Nucleotide Archive for this project ID.	dimensionless	no_bcodmo_term

Status message

Database

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Dataset: Oyster Rocks CpG