Dataset: 5a_field collection
Deployment: Kimmerer_2013

Field collection data for taxa detected in nauplii guts

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/546631/data

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Description

Description of plankton tow field collections made in San Francisco Estuary for copepod nauplii feeding studies.

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
- reformatted date and time
- rearranged columns
- sorted by sample then sequence_count (first 5 samples already sorted this way)

version 2 (2015-02-1): revised lat and lon values for site D41A
sample   site old lat old lon new lat and lon
TDN22   D41A   38.0422   -122.2438 -->38.08472, -122.3907
TDN24   D41A   38.4506   -122.2464 -->38.08472, -122.3907
TDN27   D41A   38.0749   -122.4068 -->38.08472, -122.3907

original version: 2015-01-15

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	sample sequence identification	unitless	sample
date	collection date	yyyy-mm-dd	date
time	time of collection	HH:MM	time
site	collection site	unitless	site
lat	latitude; north is positive	decimal degrees	lat
lon	longitude; east is positive	decimal degrees	lon
sal_surf	surface salinity	PSU	sal
sal_bot	bottom salinity	PSU	sal_bot
temp	temperature	degrees Celsius	temp
depth	depth	meters	depth
mesh	net mesh size	microns	net_mesh
tow_description	plankton tow type	unitless	sample_descrip
taxon_and_level	taxon and taxonomic level of collected organism	unitless	taxon
sequence_count	number of sequences of the particular taxon or group of taxa were found in the sample	sequences	count
ligase	amount of DNA ligase added	enzyme units	no_bcodmo_term

Database

Contribute Data

Dataset: 5a_field collection
Deployment: Kimmerer_2013

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: 5a_field collectionDeployment: Kimmerer_2013

Dataset acquisition description

Dataset Processing Description

Dataset: 5a_field collection
Deployment: Kimmerer_2013