Dataset: Halanych_2013_T1: NCBI accessions

Name: GenBank accession numbers used in phylogenetic analysis in Table S1, Halanych et al (2013) Nature Comm. (Antarctic Inverts project)
Published: 2016-12-22
Keywords: biota, oceans

Cite This Dataset

Project:

Genetic connectivity and biogeographic patterns of Antarctic benthic invertebrates (Antarctic Inverts)

Principal Investigator:

Kenneth M. Halanych (Auburn University)

Co-Principal Investigator:

Andrew Mahon (Central Michigan University)

BCO-DMO Data Manager:

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

Version Date:

2016-12-22

Restricted:

Validated:

Current State:

Preliminary and in progress

GenBank accession numbers used in phylogenetic analysis in Table S1, Halanych et al (2013) Nature Comm. (Antarctic Inverts project)

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Description

This dataset was published as Supplementary Table 1 from Halanych et al (2013). It contains GenBank accession links of hemichordate and echinoderm specimens collected globally from 2001 to 2013.

Related Reference: Halanych, K.M., J.T. Cannon, A.R. Mahon, B.J. Swalla, C.R. Smith. 2013. Tubicolous acorn worms from Antarctica. Nature Communications DOI://10.1038/ncomms3738

Related Dataset: Halanych_2013: Video of acorn worm tubes

Methods & Sampling

Scientific research expeditions were aboard the RVIB Nathaniel B. Palmer in 2008 to the Antarctic Peninsula and 2013 to the Ross Sea. Benthic samples were obtained from the Ross Sea by a Blake trawl with a 2-m opening. Sampled were sorted and preserved on deck. Sequencing and phylogenetic protocols of 18S and 16S ribosomal DNA used the standard procedures3. PCR amplification used primers 16Sar 50-CGCCTGTTTATCAAAAA CAT-30 and 16Sbr 50-CCGGTCTGAACTCAGATCACGT-30 for 16S ribosomal DNA and 18e 50-CTGGTTGATCCTGCCAGT-30 and 18 P 50-TAATGATCCTTCCGCAGGTTCACCT-30 .

Maximum likelihood and Bayesian analyses (both used the best fitting model GTR+I+G) were conducted with RaxML version 7.3.9 (ref. 19) (5,000 bootstrap replicates) and MrBayes version 3.2.0 (ref. 20) (four independent runs for 5,000,000 generations sampled every 100 generations), respectively.

Data Processing Description

BCO-DMO Processing notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- removed trailing blank spaces
- replaced cells with hyphen with nd (no data)
- added links to NCBI accession pages

Data Files

File
Halanych_2013_T1.csv (Comma Separated Values (.csv), 12.43 KB) MD5:a568f54b8bbb02145f894536079187e5 Primary data file for dataset ID 671551

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Office of Polar Programs (formerly NSF PLR)	PLR-1043745
NSF Office of Polar Programs (formerly NSF PLR)	PLR-1043670

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
Halanych_lab_2011-16		2011-08-01	Auburn University lab	Kenneth M. Halanych (Principal Investigator)	data info

Instruments

Automated DNA Sequencer

Supplied Name: Illumina MiSeq (San Diego, CA) at Auburn University

Supplied Description:

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

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

Supplied Name	Supplied description	Supplied Units	Standard Name
taxon	more specific taxonomic group	unitless	taxon
species	taxonomic genus and species name	unitless	species
accession_rDNA_18S	18S NCBI GenBank accession number	unitless	accession_number
accession_rDNA_16S	16S NCBI GenBank accession number	unitless	accession_number
link_accession_rDNA_18S	link to 18S NCBI GenBank accession	unitless	external_link
link_accession_rDNA_16S	link to 16S NCBI GenBank accession	unitless	external_link

Status message

Database

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Dataset: Halanych_2013_T1: NCBI accessions