Dataset: haplotype_accession_numbers
Deployment: LW_LIS08

Accession numbers for planktonic ciliate haplotypes

Principal Investigator:

George McManus (University of Connecticut, UConn - Avery Point)

Co-Principal Investigator:

BCO-DMO Data Manager:

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

Project:

Testing hypotheses about diversity, gene flow, and effective population size in marine planktonic ciliates (CiliateDivGenePop)

Current State:

Final no updates expected

Version:

14 May 2012

Version Date:

2012-05-14

Data URL:

https://www.bco-dmo.org/dataset-deployment/455187/data

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Description

Accession numbers are given for planktonic ciliate haplotypes found in Long Island Sound.

Methods & Sampling

Dataset acquisition description

Six stations were sampled in Long Island Sound on 13 August 2008. DNA was extracted and amplified. Two rDNA primers were used (OCSP-A and OCSP-B), resulting in the generation of two separate clone libraries.

More information on sample locations, methodology, and results can be found in the following publication and its supplement:
Tamura, M, LA Katz, and GB McManus. 2011. Distribution and diversity of Oligotrich and Choreotrich ciliates in a large temperate estuary. Aquat. Microb. Ecol. 64:51-67. doi:10.3354/ame01509 (PDF)

Data Processing Description

Dataset Processing Description

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-0648711	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name: Automated Sequencer

Supplied Description:

Samples were sequenced in either an ABI 3000 automated sequencer or in an ABI 377 automated sequencer.

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.

Niskin bottle

Supplied Description:

Suface samples were taken with a bucket; Niskin bottles were used to take samples below the pycnocline.

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic Description:

A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
primer_set	Name of the primer and resulting clone library.	dimensionless	no_bcodmo_term
sequence_name	Haplotype name.	dimensionless	no_bcodmo_term
accession_number	Accession number and link to GenBank.	dimensionless	accession_number

Database

Contribute Data

Dataset: haplotype_accession_numbers
Deployment: LW_LIS08

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: haplotype_accession_numbersDeployment: LW_LIS08

Dataset acquisition description

Dataset Processing Description

Dataset: haplotype_accession_numbers
Deployment: LW_LIS08