Dataset: Halanych_2013_T1: NCBI accessions
Deployment: Halanych_lab_2011-16

NCBI accessions

View Data: For data, See Dataset Metadata Page: https://www.bco-dmo.org/dataset/671551

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)

Project:

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

Version Date:

2016-12-22

Expand/Collapse All

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

Dataset acquisition description

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

Dataset 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

More information about this dataset deployment

Funding

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

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

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

Database

Contribute Data

Dataset: Halanych_2013_T1: NCBI accessions
Deployment: Halanych_lab_2011-16

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Halanych_2013_T1: NCBI accessionsDeployment: Halanych_lab_2011-16

Dataset acquisition description

Dataset Processing Description

Dataset: Halanych_2013_T1: NCBI accessions
Deployment: Halanych_lab_2011-16