Dataset: 5d_molecular id of copepod guts
Deployment: Kimmerer_2013

Identification of copepod 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://osprey.bco-dmo.org/dataset-deployment/546729/data

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Description

Field collected copepod gut content sequences were identified either by comparison to our sequence library of local copepod species or using a sequence similarity approach. Sequences were Blasted using NCBI’s web_blast.pl script (http://ncbi.nlm.nih.gov/blast/docs/web_blast.pl). The Blast output was manipulated with perl scripts we wrote to isolate the accession numbers for the BLAST hits, use the accession numbers to get the full records using NCBI’s Batch Entrez (http://www.ncbi.nlm.nih.gov/sites/batchentrez), and get the taxonomic information from the full records. See nauplii_gutcontent_sequence.pdf for the output of these programs. We then compared the taxonomic information among the top 10% BLAST scores to assign the sequence to the lowest, taxonomic level shared by the top scoring hits.

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

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
- Oithona davisae + other -->' changed to 'Oithona_davisae_and_other
- reformated date from mmm/dd/yyyy to yyyy-mm-dd
- removed commas and apostrophes

BCO-DMO data manager processing notes

* Version 2 (2021-06-10) replaces version 1 (2015-01-15). There was an unsupported character in the source file in comment "Rust_pulls_it_out_of_Fungi…". Converted to utf-8.

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
station	tow location	unitless	station
date	tow date	yyyy-mm-dd	date
contig_name	??	unitless	no_bcodmo_term
sequence_id	squence identification: sample name followed by sequence number. TDF=adult; TDN = nauplii	unitless	sample
stage	copepod life stage: N=nauplius	unitless	stage
copepod_sp	copepod species - id from SF barcode library	unitless	taxon
taxon_Perl	taxonomic id of prey item in gut using Perl program with 10% cut-off	unitless	taxon
taxon_level_Perl	taxonomic level of tax id'd from Perl	unitless	no_bcodmo_term
taxon_Claident	taxonomic id of prey items in gut using Claident with default settings against SSU_genus database	unitless	taxon
taxon_level_Claident	taxonomic level of taxon id'd with Claident	unitless	no_bcodmo_term
taxon_notes_Claident	comments on identity matching success	unitless	taxon
min_identity_SAP	minimum identity probability of prey items in gut using SAP (Statistical Assignment Program) http://ib.berkeley.edu/labs/slatkin/munch/StatisticalAssignmentPackage.html	proportion	no_bcodmo_term
posterior_prob_100_SAP	taxonomic name of SAP results for exact match	unitless	taxon
taxon_level_100_SAP	taxonomic level of taxon id'd with SAP and 100% probability	unitless	no_bcodmo_term
posterior_prob_95_100_SAP	taxonomic name of SAP results for identity probability at 95-100%	unitless	taxon
taxon_level_95_100_SAP	taxonomic level of taxon id'd with SAP and identity probability at 95-100%	unitless	no_bcodmo_term
probability	SAP probability	percent	no_bcodmo_term
warning_comment	warnings and comments from SAP run	unitless	comment

Database

Contribute Data

Dataset: 5d_molecular id of copepod guts
Deployment: Kimmerer_2013

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: 5d_molecular id of copepod gutsDeployment: Kimmerer_2013

Dataset acquisition description

Dataset Processing Description

Dataset: 5d_molecular id of copepod guts
Deployment: Kimmerer_2013