Dataset: Sulfitobacter phage accessions

Name: Roseobacter isolate Sulfitobacter sp. CB2047 and three of its infecting phage accessions at NCBI GenBank
Published: 2016-09-06
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:60.27 E:5.22 S:60.27 W:5.22

Project:

Biogeochemical implications of marine phage: Roseophage as a relevant and tractable model (Roseophage as a Model)

Principal Investigator:

Alison Buchan (University of Tennessee Knoxville, UTK)

Co-Principal Investigator:

Shawn R. Campagna (University of Tennessee Knoxville, UTK)

Steven W. Wilhelm (University of Tennessee Knoxville, UTK)

BCO-DMO Data Manager:

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

Version Date:

2016-09-06

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Roseobacter isolate Sulfitobacter sp. CB2047 and three of its infecting phage accessions at NCBI GenBank

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Description

Related Reference: Ankrah, N. Y. D., A. L. May, J. L., Middleton, D. R. Jones, M. Hadden, J. R. Gooding, G. R. LeCleir, S. W. Wilhelm, S. R. Campagna and A. Buchan. (2014 Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition. International Society for Microbial Ecology Journal (2014) 8, 1089-1100; doi:10.1038/ismej.2013.216; published online 5 December 2013

See also, Supplemental Material (PDF)

Methods & Sampling

Phage DNA was submitted to the Broad Institute and sequenced under the Gordon and Betty Moore Foundation’s Marine Phage, Virus, and Virome Sequencing Project. The Broad Institute sequencing data were assembled using the Lasergene SeqMan Pro. The assemblies resulted in the generation of single contigs for each phage genome.

The genome of Sulfitobacter sp. strain CB2047was sequenced using Illumina technology with an average sequencing coverage of approximately 600 x. The genome was assembled into 12 contigs, ranging in size from 18 kb to 2.3 Mb, using CLC Assembly Cell (CLC bio, Cambridge, MA, USA). The genome of CB2047 was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm .nih.gov/genome/annotation_prok/) and the KAAS genome annotation and pathway reconstruction server.

Data Processing Description

BCO-DMO Processing:
- added conventional header with dataset name, PI name, version date
- created a BCO-DMO servable table of accessions and associated metadata obtained from the GenBank source information.

Data Files

File
Sulfitobacter_accessions.csv (Comma Separated Values (.csv), 758 bytes) MD5:eea79644e36cbf074abeb06249f75c60 Primary data file for dataset ID 654170

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1061352

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
Buchan_lab		2011-04-01	UTenn	Alison Buchan (Principal Investigator)	data info

Instruments

Automated DNA Sequencer

Supplied Name:

Supplied Description:

Illumina HiSeq2000 at Center for Pediatric Genome Medicine Children's Mercy Hospitals and Clinics in Kansas City, MO.

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:

DNA Engine Thermo cycler (PTC-200)

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

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
taxon	taxonomic name of sequenced organism	unitless	taxon
strain	bacterial strain	unitless	taxon
description	type of genetic information	unitless	sample_descrip
date	collection date	year-month-day	date
lat	latitude; north is positive	decimal degrees	lat
lon	longitude; east is positive	decimal degrees	lon
accession_NCBI	Linked NCBI GenBank accession number	unitless	accession_number
comment	comments	unitless	comment

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Database

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Dataset: Sulfitobacter phage accessions