Dataset: Pocillopora sequences from 2019

Name: Genetic sequence accessions, collection information, and methodology for raw sequences from ezRAD libraries of Pocillopora spp. collected in Moorea, French Polynesia in 2019
Published: 2022-10-04
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.881853.1

Spatial Extent: N:-17.472 E:-149.762 S:-17.583 W:-149.924

Temporal Extent: 2019-08

Project:

Collaborative research: Coral community resilience: testing the role of hidden diversity in pocilloporid corals at Moorea (Pocilloporid Coral Diversity)

Principal Investigator:

Scott Burgess (Florida State University, FSU)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2022-10-04

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Genetic sequence accessions, collection information, and methodology for raw sequences from ezRAD libraries of Pocillopora spp. collected in Moorea, French Polynesia in 2019

Abstract:

This dataset contains genetic sequence accessions, collection information, and methodology for raw sequences from ezRAD libraries of Pocillopora spp. collected in 2019. Samples were collected between 5 and 20m on the fore reef in Moorea, French Polynesia. Sequence accessions are for holdings in the Sequence Read Archive (SRA) at the National Center for Biotechnology Information (NCBI). All sequence and biosample accessions can be found under BioProject PRJNA852278 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA852278).

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2022-10-04	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.881853.1	2022-10-12

Methods & Sampling

Tissue samples from 44 Pocillopora colonies were collected using SCUBA in August 2019 from six sites (LTER 1 – 6) and three depths (5, 10, and 20 m) around Mo’orea, French Polynesia. Tissue samples were stored in salt-saturated DMSO (dimethyl sulfoxide) buffer until DNA was extracted. Genomic DNA was extracted from tissue using the OMEGA (BIO-TEK) E.Z.N.A. Tissue DNA Kit. Extractions were quantified using the Qubit dsDNA HS Assay Kit with the Qubit Fluorometer. ezRAD libraries were generated by digesting samples with the isoschizomer restriction enzymes MboI and Sau3AI (New England BioLab), which cleave at GATC cut sites, and libraries were generated with the KAPA HyperPrep Kit (Roche) using TruSeq DNA indexes (Illumina). Libraries were size selected at 350 – 700 bp and sequenced on the MiSeq platform as paired-end 300 bp runs at Florida State University.

Data Processing Description

BCO-DMO Data manager processing notes:
* Imported file SraRunTable.txt which was generated by submitter using the NCBI run selector.
* subset columns from the run selector results

Data Files

File
pocillopora_sequences.csv (Comma Separated Values (.csv), 13.75 KB) MD5:53a07dcc6ad68595ab8ff45e654caa97 Primary data file for dataset ID 881853

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1829867

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: Illumina MiSeq

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.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
BioProject	NCBI SRA BioProject ID	unitless	BioProject
BioSample	NCBI SRA BioSample ID	unitless	BioSample
geo_loc_name	Location where sample was collected	unitless	site_descrip
Collection_Date	Year and month of collection in format (YYYY-MM) Format: %Y-%m	unitless	date
lat	Latitude of site where sample collected	decimal degrees	lat
lon	Longitude of site where sample collected	decimal degrees	lon
Depth	Depth of coral from which sample was taken	meters (m)	depth
Experiment	NCBI SRA Experiment ID	unitless	SRA_experiment
Run	SRA Run ID	unitless	SRA_run
Sample_ID	Unique ID of the sample	unitless	sample
Sample_Name	Sample name	unitless	sample
SRA_Study	NCBI SRA Study ID	unitless	SRA_study
Organism	Genus of organism	unitless	taxon
Isolate	Isolate (Coral)	unitless	sample_descrip
dev_stage	Developmental stage of the coral	unitless	sample_descrip
Tissue	Tissue sampled	unitless	sample_descrip
Assay_Type	Type of genomic library	unitless	sample_descrip
AvgSpotLen	Average spot length	unitless	sample_descrip
Bases	Size of genomic library	unitless	sample_descrip
BioSampleModel	BioSample model	unitless	sample_descrip
Bytes	Filesize in bytes for datastore file	unitless	file_size
DATASTORE_filetype	Type of file	unitless	sample_descrip
Instrument	Sequencing instrument used to create library	unitless	instrument
Isolation_Source	Coral reef habitat type where sample was collected	unitless	sample_descrip
Library_Name	Coral reef habitat type where sample was collected	unitless	sample_descrip
LibraryLayout	Paired end read samples	unitless	sample_descrip
LibrarySelection	Library selection (Reduced Representation)	unitless	sample_descrip
LibrarySource	Within cell subunit	unitless	sample_descrip
mtORF_haplotype	mitochondrial Open Reading Frame haplotype name	unitless	sample_descrip
Platform	Platform (Illumina)	unitless	sample_descrip

Database

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Dataset: Pocillopora sequences from 2019