Dataset: FRT-Dcyl-Symb_2014
Deployment: Coral_Bleaching_FRRP

Dendrogyra cylindrus 23S Illumina 2014 - relative abundance

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)

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)

Data URL:

https://www.bco-dmo.org/dataset-deployment/700141/data

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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

Dataset acquisition description

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

Dataset 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

More information about this dataset deployment

Funding

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

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

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

Contribute Data

Dataset: FRT-Dcyl-Symb_2014
Deployment: Coral_Bleaching_FRRP

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: FRT-Dcyl-Symb_2014Deployment: Coral_Bleaching_FRRP

Dataset acquisition description

Dataset Processing Description

Dataset: FRT-Dcyl-Symb_2014
Deployment: Coral_Bleaching_FRRP