Dataset: RNAseq data used to identify viral genomes

Name: RNAseq data used to identify Alphaflexivirus genomes in Stony Coral Tissue Loss Disease-affected, disease-exposed, and disease-unexposed coral colonies in the U.S. Virgin Islands (Multi-Species Coral Disease project)
Published: 2022-06-11
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.875583.1

Spatial Extent: N:18.3277 E:-64.926 S:18.3277 W:-64.926

Temporal Extent: 2019-03 - 2019-03

Project:

RAPID: Collaborative Research: Predicting the Spread of Multi-Species Coral Disease Using Species Immune Traits (Multi-Species Coral Disease)

Principal Investigator:

Laura Mydlarz (University of Texas at Arlington, UT Arlington)

Co-Principal Investigator:

Adrienne M.S. Correa (Rice University)

Contact:

Kelsey Beavers (University of Texas at Arlington, UT Arlington)

BCO-DMO Data Manager:

Sawyer Newman (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2022-06-11

Restricted:

Validated:

Yes

Current State:

Final no updates expected

RNAseq data used to identify Alphaflexivirus genomes in Stony Coral Tissue Loss Disease-affected, disease-exposed, and disease-unexposed coral colonies in the U.S. Virgin Islands (Multi-Species Coral Disease project)

Abstract:

RNA-seq data from healthy, SCTLD-exposed, and SCTLD-infected coral samples taken from a transmission experiment carried out in the US Virgin Islands.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2022-06-11	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.875583.1	2022-06-14

Methods & Sampling

Methodology:

Sampling and analytical procedures:

A SCTLD transmission experiment was carried out at the University of the Virgin Islands (UVI) in April of 2019 and is described in Meiling et al. (2021). One fragment from 6 species of stony coral was placed into a control mesocosm equidistant from a central healthy coral colony. Corresponding genet fragments were placed into an experimental mesocosm equidistant from a SCTLD-infected coral colony. This paired design was replicated for a total of 8 genets per species. Experimental coral fragments that developed lesions were removed and stored at -80ºC for RNA sequencing when 30% tissue loss was achieved. Corresponding control coral fragments were removed and stored at the same time. Tissue samples were harvested from the fragments and total RNA was extracted using the RNAqeous-4PCR total RNA isolation kit (Invitrogen, Life Technologies AM1914) as explained in Veglia et al. (2022). Tissues were lysed using a refrigerated Qiagen TissueLyser II micro centrifuge at 30 oscillations per second for 30 s. Contaminating DNA and chromatin were removed from the total RNA using the Ambion DNase I (RNase-free) kit (Invitrogen, Life Technologies AM2222). Samples were preprocessed by Novogene Co., Ltd. for mRNA enrichment using polyA tail capture; the mRNA libraries underwent 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 instrument using the NEBNext Ultra II RNA library prep kit.

Data Processing Description

Processing notes from researcher:

BBSplit was used to map quality-filtered (fast v0.20.1) reads to coral or Symbiodiniaceae transcriptome and generate three read files: (I) coral, (ii) Symbiodiniaceae, and (iii) noncoral/non-Symbiodiniaceae. Noncoral/non-Symbiodiniaceae reads were uploaded to NCBI.

BCO-DMO processing description:

Converted dates to YYYY-MM-DD or YYYY-MM formats where appropriate
Removed apostrophes (') from Dive_Site column
Replaced spaces (" ") with underscores (_) in column headers
Converted lat and long from degrees, hours, seconds to decimal degrees format (64˚55'33.5"W → -64.925972)

Data Files

File
bco_dmo_sampleinfo-1.csv (Comma Separated Values (.csv), 1.52 KB) MD5:1af5b24c78fd32bdc996f7e9799f896b Primary data file for dataset ID 875583

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1928771

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: Illumina NovaSeq 6000

Supplied Description:

An Illumina NovaSeq 6000 was used for 150-bp, pared-end mRNA sequencing

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.

Qiagen TissueLyser II

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Qiagen TissueLyser II

Generic Description:

The Qiagen TissueLyser II is a tissue processor designed to disrupt biological samples through high-speed shaking in plastic tubes with stainless steel, tungsten carbide, or glass beads. It is used for high-throughput disruption of human, animal, and plant tissues, bacteria, and yeast to access biological information for genomics, transcriptomics, and proteomics applications. It automates the purification of DNA, RNA, and protein from 1 to 96 samples. Disruption and homogenization are achieved through the beating and grinding effect of beads on the sample material as they are shaken together in the grinding vessels. Using the appropriate adapter set, up to 48 or 192 samples can be processed at the same time. Alternatively, a grinding jar set can be used to process large samples. A range of beads, bead dispensers, and collection microtubes and caps are also available. It can be programmed to provide variable speeds from 3 to 30 Hz (180-1800 oscillations per minute) and run times from 10 seconds to 99 minutes.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Sample_Name	Sample ID	unitless	sample
Organism	Coral species	unitless	species
Dive_Site	Dive site common name	unitless	site
Lat	Latitude of dive site in decimal degrees, a positive value indicates North	decimal degrees	lat
Lon	Longitude of dive site in decimal degrees, a negative value indicates West	decimal degrees	lon
Collection_Date	Date collected from the reef; %Y-%M Format: %Y-%m	unitless	date
Experiment_Mesocosm	The mesocosm the coral fragment went in (conrol or disease; bins 1 through 8)	unitless	treatment
Freeze_Date	Date the coral was removed from the experiment and flash frozen; %Y-%M-%D Format: %Y-%m-%d	unitless	date
Accession	BioProject Accession ID	units	BioProject
SRA	SRA ID	unitless	SRA_sample

Status message

Database

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Dataset: RNAseq data used to identify viral genomes