Dataset: NCBI accession numbers for RNAseq data from five coral species experimentally exposed to SCTLD

Name: NCBI accession numbers for RNAseq data from five coral species experimentally exposed to Stony Coral Tissue Loss Disease (SCTLD) at the University of the Virgin Islands in 2019
Published: 2022-09-30
Keywords: RNAseq, SCTLD, immunity, disease, stony coral tissue loss disease, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.881776.1

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

Temporal Extent: 2019-03-17 - 2019-04-12

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)

Student:

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

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2022-09-30

Restricted:

Validated:

Yes

Current State:

Final no updates expected

NCBI accession numbers for RNAseq data from five coral species experimentally exposed to Stony Coral Tissue Loss Disease (SCTLD) at the University of the Virgin Islands in 2019

Abstract:

Raw RNA sequence data were obtained from a disease transmission experiment carried out at the University of the Virgin Islands in which five reef-building coral species, Colpophyllia natans, Orbicella annularis, Pseudodiploria strigosa, Porites astreoides, and Montastraea cavernosa, were exposed to Stony Coral Tissue Loss Disease (SCTLD) in mesocosms. Sequences were used to compare the differential expression of host and endosymbiont genes between disease states (control, disease-exposed, and disease-infected) and to elucidate a transcriptomic model of the holobiont response to SCTLD. This dataset includes National Center for Biotechnology Information (NCBI) accession numbers and related data for those five coral species examined in the experiment.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2022-09-30	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.881776.1	2022-10-05

Methods & Sampling

A Stony Coral Tissue Loss Disease (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).

Coral colonies were collected from Rupert's Rock Reef (18.3277 N, -64.926 E) from March 17 to April 02 of 2019. One fragment from five 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 microcentrifuge at 30 oscillations per second for 30 seconds. 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

BCO-DMO Processing:
- converted date columns to YYYY-MM-DD format.

Data Files

File
accessions_five_coral_species.csv (Comma Separated Values (.csv), 7.09 KB) MD5:ee26dbba27afcfe6a9bf034fbf1f8df0 Primary data file for dataset ID 881776

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:

mRNA libraries underwent 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 instrument.

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 Description:

Tissues were lysed using a refrigerated Qiagen TissueLyser II.

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 number	unitless	sample
Organism	Coral species	unitless	species
Dive_Site	Dive site where the colony was taken	unitless	site
Lat	Latitude where the colony was taken	degrees North	lat
Lon	Longitude where the colony was taken	degrees East	lon
Collection_Date	Date of colony collection in format YYYY-MM-DD; time zone: Atlantic Standard Time (AST) Format: %Y-%m-%d	unitless	date
Experiment_Mesocosm	Mesocosm (Control or Diseased; #1-8) where the fragment was placed	unitless	tank
Freeze_Date	Date of fragment removal from experiment and freezing in format YYYY-MM-DD; time zone: Atlantic Standard Time (AST) Format: %Y-%m-%d	unitless	date
BioProject	NCBI BioProject number	unitless	BioProject
Biosample_Accession	NCBI BioSample accession number	unitless	BioSample
SRA_accession	NCBI SRA accession number	unitless	SRA_sample

Database

Contribute Data

Dataset: NCBI accession numbers for RNAseq data from five coral species experimentally exposed to SCTLD