Dataset: Virus dPCR assay primers
Deployment: Bigelow_Martinez_2015-2016

Primers used for Pleurochrysis carterae virus dPCR assays

View Data: For data, See Dataset Metadata Page: https://osprey.bco-dmo.org/dataset/670450

Principal Investigator:

Joaquín Martínez Martínez (Bigelow Laboratory for Ocean Sciences)

Contact:

Joaquín Martínez Martínez (Bigelow Laboratory for Ocean Sciences)

BCO-DMO Data Manager:

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

Project:

Persistent Virus Infections in Marine Phytoplankton (Marine Chronic Viruses)

Current State:

Preliminary and in progress

Version:

Expand/Collapse All

Description

This dataset includes information for the five primers used in the Pleurochrysis carterae virus production dataset. It contains the primer ID, forward primer, reverse primer, amplicon length, annealing temperature, and probe amplicon sequence.

Methods & Sampling

Dataset acquisition description

Probes and primers were designed to target genotypes: Pleurochrysis carterae endemic virus genotypes 2 and 1b (PsEV2 and PsEV1b, respectively; dsDNA viruses); P. carterae Polinton-like viruses (PleuroPLV; dsDNA viruses); and P. carterae CRESS viruses (PcCV1, ssDNA viruses). For the latter, we designed probes for both the REP and the CAP genes to discriminate viral particles with partial (i.e., amplification for only the REP or the CAP markers from a single dPCR intact drop) or complete genomes (i.e., amplification with both molecular markers from a single dPCR intact drop).

Deployment-specific acquisition description

laboratory experiment

Data Processing Description

Dataset Processing Description

BCO-DMO Data Manager Processing Notes:
* made primer PcCV-1_Rep sequence uppercase (AGGAGGAG...)to match all other sequence formatting.
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions
* blank values replaced with no data value 'nd'

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1346272	NSF Division of Ocean Sciences

Instruments

None available yet

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
primer_id	Primer identifier (see dataset acquisition section for details)	unitless	sample
forward_primer	Forward primer sequence	unitless	sequence
reverse_primer	Reverse primer sequence	unitless	sequence
aplicon_length	Number of nucleobases in amplicon	unitless	sequence
annealing_temp	Annealing temperature	degrees Celsius	temp
probe	Probe sequence	unitless	sequence
amplicon_sequence	Amplicon sequence	unitless	sequence

Database

Contribute Data

Dataset: Virus dPCR assay primers
Deployment: Bigelow_Martinez_2015-2016

Dataset acquisition description

Deployment-specific acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Virus dPCR assay primersDeployment: Bigelow_Martinez_2015-2016

Dataset acquisition description

Deployment-specific acquisition description

Dataset Processing Description

Dataset: Virus dPCR assay primers
Deployment: Bigelow_Martinez_2015-2016