Dataset: 5c_BLAST results
Deployment: Kimmerer_2013

GenBank BLAST results of copepod nauplii gut contents

Principal Investigator:

William Kimmerer (San Francisco State University, SFSU)

Co-Principal Investigator:

Sarah Cohen (San Francisco State University, SFSU)

BCO-DMO Data Manager:

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

Project:

Feeding and food limitation in copepod nauplii, the neglected life stage (food limitation in copepod nauplii)

Current State:

Final no updates expected

Version:

2015-01-15

Version Date:

2015-01-15

Data URL:

https://www.bco-dmo.org/dataset-deployment/546677/data

Expand/Collapse All

Description

Field collected copepod nauplii gut content sequences were identified using the BLASTN algorithm on GenBank or by comparison to a sequence library of local copepod species constructed for this project. Blast searches of the GenBank database were conducted on May 16, 2013. BLASTed sequences were identified to the taxonomic level at which there was consensus among matches within 10% of the best score.

Related Reference:

* Craig, Carrie, Wim J. Kimmerer, and C. Sarah Cohen. 2014. A DNA-based method for investigating feeding by copepod nauplii. Journal of Plankton Research 36 (1): 271-275

Vogt, R.A., T.R. Ignoffo, L.J. Sullivan, J. Herndon, J.H. Stillman, and W. Kimmerer. 2013. Feeding capabilities and limitations in the nauplii of two pelagic estuarine copepods, Pseudodiaptomus marinus and Oithona davisae. Limnology and Oceanography 58: 2145-2157.

Methods & Sampling

Dataset acquisition description

See Methodology (pdf).

Data Processing Description

Dataset Processing Description

BCO-DMO Processing:
- added conventional header with dataset name, PI name, version date, reference information
- renamed parameters to BCO-DMO standard
- replaced blanks with underscores
- moved sequence id's to separate column
- replaced '?' with '_maybe'
- changed Pseudodioptamus to Pseudodiaptomus

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-0929075	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name: Automated Sequencer

Supplied Description:

ABI 3130 Genetic Analyzer

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.

High-Performance Liquid Chromatograph

Supplied Name: HPLC

Supplied Description:

Instrument Type

Generic Name: High-Performance Liquid Chromatograph

Acronym: HPLC

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB11/

Generic Description:

A High-performance liquid chromatograph (HPLC) is a type of liquid chromatography used to separate compounds that are dissolved in solution. HPLC instruments consist of a reservoir of the mobile phase, a pump, an injector, a separation column, and a detector. Compounds are separated by high pressure pumping of the sample mixture onto a column packed with microspheres coated with the stationary phase. The different components in the mixture pass through the column at different rates due to differences in their partitioning behavior between the mobile liquid phase and the stationary phase.

Plankton Net

Supplied Description:

Mesh size 100 microns or 150 microns

Instrument Type

Generic Name: Plankton Net

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/22/

Generic Description:

A Plankton Net is a generic term for a sampling net that is used to collect plankton. It is used only when detailed instrument documentation is not available.

Thermal Cycler

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

Supplied Name	Supplied description	Supplied Units	Standard Name
sequence_id	squence identification: sample name followed by sequence number. TDF=adult; TDN = nauplii	unitless	sample
GenBank_id	GenBank accession number of BLAST hit	unitless	accession_number
BLAST_score	BLAST score: statistical significance of sequence matches to GenBank database	unitless	no_bcodmo_term
domain	taxonomic domain: Bacteria or Eukaryota	unitless	taxon
tax_rank_1	highest taxonomic name	unitless	taxon
tax_rank_2	taxonomic name; more specific than preceeding	unitless	taxon
tax_rank_3	taxonomic name; more specific than preceeding	unitless	taxon
tax_rank_4	taxonomic name; more specific than preceeding	unitless	taxon
tax_rank_5	taxonomic name; more specific than preceeding	unitless	taxon
tax_rank_6	taxonomic name; more specific than preceeding	unitless	taxon
tax_rank_7	taxonomic name; more specific than preceeding	unitless	taxon
tax_rank_8	taxonomic name; more specific than preceeding	unitless	taxon
tax_rank_9	taxonomic name; more specific than preceeding	unitless	taxon
tax_rank_10	taxonomic name; more specific than preceeding	unitless	taxon
tax_rank_11	taxonomic name; more specific than preceeding	unitless	taxon
tax_rank_12	taxonomic name; more specific than preceeding	unitless	taxon
tax_rank_13	taxonomic name; more specific than preceeding	unitless	taxon
tax_rank_14	taxonomic name; more specific than preceeding	unitless	taxon
tax_rank_15	taxonomic name; more specific than preceeding	unitless	taxon
tax_rank_16	taxonomic name; more specific than preceeding	unitless	taxon

Database

Contribute Data

Dataset: 5c_BLAST results
Deployment: Kimmerer_2013

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: 5c_BLAST resultsDeployment: Kimmerer_2013

Dataset acquisition description

Dataset Processing Description

Dataset: 5c_BLAST results
Deployment: Kimmerer_2013