Dataset: planktonic ciliates: DNA accessions
Deployment: CH0112

Planktonic ciliate DNA sequence accession numbers at NCBI GenBank

Principal Investigator:

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

Co-Principal Investigator:

Laura A. Katz (Smith College)

Scientist:

Luciana Santoferrara (University of Connecticut, UConn - Avery Point)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Diversity and dynamics of planktonic ciliates - what can next-generation sequencing technologies tell us? (CiliateSequencing)

Version Date:

2015-11-19

Data URL:

https://www.bco-dmo.org/dataset-deployment/626700/data

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Description

This dataset includes 4 sets of NCBI accession numbers for planktonic ciliates. Some of the links to the NCBI pages are not yet live.

Contact for the single cells from Long Island Sound: Luciana Santoferrara, post-doc: luciana.santoferrara_at_uconn.edu. Contact for the other data: George McManus.

Methods & Sampling

Dataset acquisition description

DGGE_Weiker: Surface samples were collected while following a surface drifter (crosse window shade type). DNA was extracted and amplified with PCR, and amplicons were separated with denaturant gradient gel electrophoresis. Sequencing use the Sanger method. Details can be found in Grattepanche, et al, 2014.

454 Long Island Sound: Surface and deep samples were taken from the Sound on several occasions. DNA was extracted and a ciliate clade-specific portion of the small subunit ribosomal gene was amplified using the polymerase chain reaction. Amplified fragments were sequenced using the Roche 454 platform. Details are reported in Santoferrara, et al, 2014.

454 and DGGE Hatteras: Vertically-resolved samples were collected along a section due south from Naragansett RI to the shelf break. DNA was extracted and amplified with PCR, and amplicons were separated with denaturant gradient gel electrophoresis or sequenced with Roche 454. Methodological details can be found in Grattepanche, et al, 2014 and Santoferrara, et al, 2014.

Single cells, Long Island Sound: Individual cells of tintinnid microzooplankton were picked with a micropipette, photo documented and placed in buffer for extraction and sequencing. Sequences of the internal transcribed spacer regions (ITS1-5.8S-ITS2), the small sub unit ribosomal gene (SSU), and the large subunit ribosomal gene (LSU) were obtained by Sanger sequencing.

References:

Grattepanche, J-D, L Santoferrara, J Andrade, AM Oliverio, GB McManus, and LA Katz. 2014. Distribution and diversity of oligotrich and choreotrich ciliates assessed by morphology and by DGGE in temperate coastal waters. Aquat. Microb. Ecol. 71:211-221. DOI:10.3354/ame01675.

Santoferrara, L, J-D Grattepanche, LA Katz, and GB McManus. 2014. Pyrosequencing for assessing diversity of eukaryotic microbes: analysis of data on marine planktonic ciliates and comparison with traditional methods. Environ. Microbiol. DOI: 10.1111/1462-2920.12380.

Santoferrara, LF, GB McManus, and VA Alder. 2012. Utility of Genetic Markers and Morphology for Species Discrimination within the Order Tintinnida (Ciliophora, Spirotrichea). Protist , doi:10.1016/j.protis.2011.12.002

Data Processing Description

Dataset Processing Description

DGGE_Weiker: Raw chromatograms were checked by eye and fragments were assembled into contains using LaserGene.

454 Long Island Sound: Sequences were processed in QIIME using a quality score of 37 without clustering.

454 and DGGE Hatteras: For DGGE, raw chromatograms were checked by eye and fragments were assembled into contains using LaserGene. For 454 data, sequences were processed in QIIME using a quality score of 37 and without clustering.

Single cells, Long Island Sound: Raw chromatograms were edited by eye and contains were assembled using MEGA. Details can be found in Santoferrara, et al, 2012.

BCO-DMO Processing:
- Created a table with columns: dataset_id, location, lat, lon, cruise_id, date, description, comment, accession_number.
- Created links to the accessions.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1130033	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name:

Supplied Description:

Roche 454 platform and others

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.

Thermal Cycler

Supplied Name:

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
dataset_id	name of dataset	unitless	dataset_id
location	location of sample collection	unitless	site
lat	latitude; north is positive	decimal degrees	lat
lon	longitude; east is positive	decimal degrees	lon
cruise_id	cruise identification	unitless	cruise_id
date	date of collection	yyyy-mm-dd	date
description	DGGE: Denaturing Gradient Gel Electrophoresis; ITS: Internal Transcribed Spacer region of the ribosomal gene (ITS1-5.8S-ITS2); SSU: Small Sub-Unit of the ribosomal gene; LSU: Large Sub-Unit of the ribosomal gene	unitless	no_bcodmo_term
comment	comment	unitless	comment
NCBI_accession	NCBI accession number	unitless	accession_number

Database

Contribute Data

Dataset: planktonic ciliates: DNA accessions
Deployment: CH0112

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: planktonic ciliates: DNA accessionsDeployment: CH0112

Dataset acquisition description

Dataset Processing Description

Dataset: planktonic ciliates: DNA accessions
Deployment: CH0112