Dataset: Metabarcoding zooplankton at station ALOHA: NCBI SRA accession numbers

Name: NCBI Sequence Read Archive (SRA) accession numbers for fastq sequence files for each zooplankton community sample (Plankton Population Genetics project)
Published: 2017-05-25
Keywords: Metabarcoding, station ALOHA, mesopelagic and bathypelagic zooplankton, community composition, oceans

Cite This Dataset

DOI:10.1575/1912/bco-dmo.704665

Spatial Extent: N:22.75 E:-158 S:22.75 W:-158

Temporal Extent: 2014-06-13 - 2014-06-19

Project:

Basin-scale genetics of marine zooplankton (Plankton Population Genetics)

Principal Investigator:

Erica Goetze (University of Hawai'i, UH)

Contact:

Erica Goetze (University of Hawai'i, UH)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version Date:

2017-05-25

Restricted:

Validated:

Yes

Current State:

Final no updates expected

NCBI Sequence Read Archive (SRA) accession numbers for fastq sequence files for each zooplankton community sample (Plankton Population Genetics project)

Expand/Collapse All

Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2017-05-25	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.1575/1912/bco-dmo.704665	2017-06-12

Description

These data include sample information and accession links to sequence data at The National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA).

This data submission consists of metabarcoding data for the zooplankton community in the epipelagic, mesopelagic and upper bathypelagic zones (0-1500m) of the North Pacific Subtropical Gyre. The goal of this study was to assess the hidden diversity present in zooplankton assemblages in midwaters, and detect vertical gradients in species richness, depth distributions, and community composition of the full zooplankton assemblage. Samples were collected in June 2014 from Station ALOHA (22.75, -158) using a 1 meter square Multiple Opening and Closing Nets and Environmental Sampling System (MOCNESS, 200um mesh), on R/V Falkor cruise FK140613. Next generation sequence data (Illumina MiSeq, V3 chemistry, 300-bp paired-end) of the zooplankton assemblage derive from amplicons of the V1-V2 region of 18S rRNA (primers described in Fonseca et al. 2010). The data includes sequences and read count abundance information for molecular OTUs from both holoplanktonic and meroplanktonic taxa

Related dataset containing OTU tables and fasta sequences (representative / most abundance read for each OTU):
Metabarcoding zooplankton at station ALOHA: OTU tables and fasta files

Methods & Sampling

SAMPLE INFORMATION

Sample identifiers include the following codes.

MOCNESS tow
FA3: Night sampling
FA4: Day sampling

Depth range:
N1: 1500-1000m
N2: 1000-700m
N3: 700-500m
N4: 500-300m
N5: 300-200m
N6: 200-150m
N7: 150-100m
N8: 100-50m
N9: 50m-0m

Wet-sieved zooplankton size fractions
SF1: 0.2-0.5 mm
SF2: 0.5-1.0 mm
SF3: 1.0-2.0 mm

Data Processing Description

BCO-DMO processing notes:
* commas in the data were replaced with semicolons to support export as csv format.

Data Files

File
SRA.csv (Comma Separated Values (.csv), 20.94 KB) MD5:22200d6c11cd04c32cf3a29e3d687956 Primary data file for dataset ID 700961

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1338959
NSF Division of Ocean Sciences	OCE-1255697
NSF Division of Ocean Sciences	OCE-1029478

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
FK140613		2014-06-13	R/V Falkor	Erica Goetze (Chief Scientist)	data info

Instruments

Automated DNA Sequencer

Supplied Name: Illumina MiSeq

Supplied Description:

Illumina MiSeq using V3 chemistry (300-bp, paired-end)

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.

Bioanalyzer

Supplied Name: Agilent 2100 Bioanalyzer

Supplied Description:

Instrument Type

Generic Name: Bioanalyzer

Generic Description:

A Bioanalyzer is a laboratory instrument that provides the sizing and quantification of DNA, RNA, and proteins. One example is the Agilent Bioanalyzer 2100.

Thermal Cycler

Supplied Name: quantitative PCR by the Evolutionary Genetics Core Facility (Hawaii Institute of Marine Biology)

Supplied Description:

Instrument Type

Generic Name: Thermal Cycler

Generic Description:

A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
analysis_name	Descriptive name of analysis including percent clustering and subsampling or no subsampling	unitless	sample_descrip
lat	Latitude of sample site (Station ALOHA)	decimal degrees	lat
lon	Longitude of sample site (Station ALOHA)	decimal degrees	lon
library_ID	Short unique identifier for the sequencing library.	unitless	sample
bioproject_accession	NCBI BioProject identifier	unitless	accession_number
biosample_accession	NCBI BioSample identifier	unitless	accession_number
title	Short description that will identify the dataset on public pages.	unitless	sample_descrip
library_strategy	Amplicon = Sequencing of overlapping or distinct PCR or RT-PCR products	unitless	sample_descrip
library_source	Metagenomic = Mixed material from metagenome	unitless	sample_descrip
library_selection	PCR = Source material was selected by designed primers	unitless	sample_descrip
library_layout	Paired-end or Single	unitless	sample_descrip
platform	Sequencing platforms [Illumina]	unitless	sample_descrip
instrument_model	Illumina instrument and model used for sequencing	unitless	instrument
design_description	Free-form description of the methods used to create the sequencing library; a brief materials and methods section.	unitless	sample_descrip
bioproject_link	bioproject_link	unitless	no_bcodmo_term
biosample_link	biosample_link	unitless	no_bcodmo_term

Status message

Database

Contribute Data

Dataset: Metabarcoding zooplankton at station ALOHA: NCBI SRA accession numbers