Dataset: FRT-Dcyl-Symb_2014

Name: Symbiodinium species and relative abundance in Dendrogyra cylindrus from 3 regions of the Florida Reef Tract, April 2014 (EMUCoReS project)
Published: 2017-05-17
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:25 E:-80.4 S:24.47 W:-81.75

Temporal Extent: 2014-04-01 - 2014-12-30

Project:

RAPID: A hyper-thermal anomaly in the Florida Reef Tract: An opportunity to explore the mechanisms underpinning patterns of coral bleaching and disease (EMUCoReS)

Principal Investigator:

Dr Mauricio Rodriguez-Lanetty (Florida International University, FIU)

Co-Principal Investigator:

Dr Diego Lirman (University of Miami Rosenstiel School of Marine and Atmospheric Science, UM-RSMAS)

Dr Laurie Richardson (Florida International University, FIU)

BCO-DMO Data Manager:

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

Version Date:

2017-05-17

Restricted:

Validated:

Current State:

Preliminary and in progress

Symbiodinium species and relative abundance in Dendrogyra cylindrus from 3 regions of the Florida Reef Tract, April 2014 (EMUCoReS project)

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Description

This dataset includes the relative abundance of Dendrogyra cylindrus which were analyzed for 23S on an Illumina platform from three sites in the Florida Reef Tract, one each in the upper, middle and lower Keys in 2014.

Methods & Sampling

Dendrogyra cylindrus tissue sampling: syringe micro-sampling method (described in Kemp et al. 2008); samples filtered with Swinnex filter holder (13mm) with 3.0µm glass fiber filter; filter preserved in 95% ETOH.

DNA extraction: DNeasy Plant Mini kit (Qiagen) with modifications:
5 min bead beating – acid-washed glass beads
20µl Proteinase K - incubate 1 hr at 56°C

amplicon sequencing: partial chloroplast large subunit 23S rDNA Domain V gene hyper-variable region (Santos et al 2003)

Data Processing Description

MR DNA analysis pipeline: MR DNA, Shallowater, TX, USA
Mothur software v1.37.2 (Schloss e t al. 2009) Operational taxonomic units (OTUs) generated, 0.03 similarity cutoff

BCO-DMO Processing Notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions

Data Files

File
abund_Dcyl_Symb_2014.csv (Comma Separated Values (.csv), 4.52 MB) MD5:e1152a942a931e05222d9e8f40504440 Primary data file for dataset ID 700133

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1503430
NSF Division of Ocean Sciences	OCE-1503483

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
Coral_Bleaching_FRRP		2014-01-01	shoreside Florida_Coral_Reefs	Dr Mauricio Rodriguez-Lanetty (Principal Investigator)	data info

Instruments

Automated DNA Sequencer

Supplied Name: Illumina Mi-Seq - MR.DNA Next Generation Sequencing, Shallowater, Texas (www.mrdnalab.com)

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
OTU_id	operational taxonomic unit identity	unitless	sample
species	Symbiodinium species identification	unitless	taxon
sample_6_thru_499	relative abundance of OTU	percent	relative_abund

Database

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Dataset: FRT-Dcyl-Symb_2014