Dataset: Diatom microbiome
Deployment: SantaCruz_Plankton_Jiang

Identification of microbiome from different Pseudo-nitzschia species

Principal Investigator:

Sunny Jiang (University of California-Irvine, UC Irvine)

BCO-DMO Data Manager:

Danie Kinkade (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Interactions of bacteria, viruses and bloom-forming diatom genus Pseudo-nitzschia (bacteria, virus, diatom interactions)

Current State:

Final no updates expected

Version:

2015-08-05

Version Date:

2015-08-05

Data URL:

https://www.bco-dmo.org/dataset-deployment/614792/data

Expand/Collapse All

Description

Methods & Sampling

Dataset acquisition description

Bacterial total genome DNA was extracted from the single species Pseudo-nitzschia culture. 16S rDNA pyrosequencing were carried out using the bTEFAP method based on the Titanium reagents and protocol for Genome Sequencer FLX System.

Data Processing Description

Dataset Processing Description

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1131770	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name: Seqman II

Supplied Description:

A Seqman II (version 9.0 DNASTAR Inc, Madison, WI, USA) was used for sequencing of bacterial 16s rDNA.

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.

Automated DNA Sequencer

Supplied Name: Genome Sequencer FLX System

Supplied Description:

Genome Sequencer FLX System was used for pyroseqencing of pseudo-nitzschia microbiome.

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

Microscope - Optical

Supplied Name: Light Microscope

Supplied Description:

Instrument Type

Generic Name: Microscope - Optical

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/

Generic Description:

Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope".

Plankton Net

Supplied Description:

20um mesh size plankton net was used for sampling.

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 Name: GeneAmp 2700 PCR system

Supplied Description:

GeneAmp 2700 PCR system (Applied Biosystems, Foster City, CA) was used for PCR amplification.

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 Units	Standard Name
project_type	dimensionless	project
attributes	dimensionless	no_bcodmo_term
NCBI_bioproject_id	dimensionless	accession_number

Database

Contribute Data

Dataset: Diatom microbiome
Deployment: SantaCruz_Plankton_Jiang

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Diatom microbiomeDeployment: SantaCruz_Plankton_Jiang

Dataset acquisition description

Dataset Processing Description

Dataset: Diatom microbiome
Deployment: SantaCruz_Plankton_Jiang