Species names, sample codes, and collection details for sequenced sea slugs in the family Oxynoidae that were used in phylogenetic analyses. Collections range from 1974 to 2014 from global locations near Florida, the Caribbean, and the East and West Pacific Ocean. Data are accessioned through the NCBI GenBank database.

Methods & Sampling

Purified PCR products were directly cycle-sequenced in both directions using PCR primers and Big Dye Terminator 3.1 Cycle Sequencing chemistry Retrogen, Inc. (San Diego). Chromatograms were edited and primer sequences removed in GeneiousPro 4.8 software. Samples for morphological analysis were deposited in museum collections, sequences were archived in GenBank for public access.

Data Files

File
dataset8.csv (Comma Separated Values (.csv), 16.47 KB) MD5:9b4af5b5dcd8d610cf10429207e9d85b Primary data file for dataset ID 715506

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1130072

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: Automated sequencer

Supplied Description:

Big Dye Terminator 3.1 Cycle Sequencing chemistry Retrogen, Inc. (San Diego)

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
species	Species	unitless	species
isolate_code	Isolate code	unitless	sample
specimen_accession_numbers	Accession numbers. 1AM = Australian Museum (Sydney, Australia) malacology collection; LACM = Los Angeles County Museum of Natural History malacology collection.	unitless	accession_number
collection_site	Collection site	unitless	site
date	Date	unitless	date
collector	Collector's name. AAV = Angel A. Valdes; AH = Alicia Hermosillo; CDT = Cynthia D. Trowbridge; DH = Dai Herbert; DJM = Dustin J. Marshall; MAP = Mark A. Phuong; NGW = Nerida G. Wilson; PJK = Patrick Joseph Krug; RAE = Ryan A. Ellingson; YB = Yan Buske; YMH = Yayoi M. Hirano	unitless	person
accession_COI	COI gene GenBank accession number	unitless	accession_number
accession_16S	16S gene GenBank accession number	unitless	accession_number
accession_H3	H3 gene GenBank accession number	unitless	accession_number