Dataset: Metagenome of Bleached and Non-bleached corals

Name: Sample and treatment information for the environmental metagenome of paired bleaching and nonbleaching Pocillopora cf. meandrina corals in Mo'orea, French Polynesia in March of 2016
Published: 2021-03-12
Keywords: coral bleaching, microbiome, Virome, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.844868.1

Spatial Extent: N:-17.28 E:-149.49 S:-17.28 W:-149.49

Temporal Extent: 2016-03

Project:

Collaborative Research: Viral Reefscapes: The Role of Viruses in Coral Reef Health, Disease, and Biogeochemical Cycling (Moorea Virus Project)

Principal Investigator:

Andrew Thurber (Oregon State University, OSU-CEOAS)

Student:

Adriana Messyasz (Oregon State University, OSU)

Contact:

Adriana Messyasz (Oregon State University, OSU)

Data Manager:

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

Version:

Version Date:

2021-03-12

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Sample and treatment information for the environmental metagenome of paired bleaching and nonbleaching Pocillopora cf. meandrina corals in Mo'orea, French Polynesia in March of 2016

Abstract:

Sample and treatment information for the environmental metagenome of paired bleaching and nonbleaching Pocillopora cf. meandrina corals in Mo'orea, French Polynesia in March of 2016. All sequences are available in the Short Read Archive (SRA) at The National Center for Biotechnology Information (NCBI)under BioProject PRJNA647466 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA647466).

Expand/Collapse All

Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2021-03-12	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.844868.1	2021-03-17

Description

A processed version of these data were published in Messyasz et al. (2020) (all tables and figures).

All sequences are available in the Short Read Archive (SRA) at The National Center for Biotechnology Information (NCBI). BioSample and SRA accessions can be accessed from the BioProject PRJNA647466 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA647466).

Methods & Sampling

Location: Mo’orea, French Polynesia, Pacific Ocean.

Sampling and analytical procedures:

Pocillopora spp. coral fragments were collected in situ on SCUBA using bone-cutters. For each coral sample, fragments were airbrushed with 1.5 mL of Qiagen Dneasy Kit lysis buffer and the resulting coral tissue slurry was used for whole community DNA extraction with a Dneasy Kit. For metagenome generation, the extracted DNA from the coral fragments were cleaned with Zymo DNA Clean and Concentrator- 5 Kits and eluted into Ultra-pure H2O for sequencing. DNA from each coral sample was prepared for sequencing with the PrepX DNA Library Kit, then sequenced on the Illumina HiSeq 3000 platform (2 × 150 paired-end).

Data Processing Description

The only data processing was done by the sequencing facility which included stripping of sequencing primers and bar codes. No other data manipulation was done.

BCO-DMO Data Manager Notes:
* Data in file "biosample_result.txt" imported into the BCO-DMO data system.
* Sample latitude, longitude, year and month added to the data table from information under the BioSamples at NCBI.
* Modified parameter (column) names to conform with BCO-DMO naming conventions: only A-Za-z0-9 and underscore allowed. Can not start with a number. (spaces, +, and - changed to underscores).
* Converted Date format to ISO 8601 format yyyy-mm-dd

Data Files

File
sra_bleach_nonbleach.csv (Comma Separated Values (.csv), 694 bytes) MD5:343cd85f84a8d111bc7ddcd185a1a259 Primary data file for dataset ID 844868

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1635913
NSF Division of Ocean Sciences	OCE-1635798

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: Illumina HiSeq 3000

Supplied Description:

Sequencing was performed on the Illumina HiSeq 3000 sequencing platform at the Center for Genome Research and Biocomputing at Oregon State University.

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
BioSample	BioSample accession identifier at NCBI. The associated Sequence Read Archive (SRA) sequences can be found by searching by BioSample.	unitless	accession_number
Treatment	Corals were either bleached (having lost their photosynthetic symbionts) or non-bleached.	unitless	sample_descrip
Replicate	Paired corals were collected adjacent to each other with one being bleached and the other not. Corals with the same replicate ID were adjacent to each other on the reef at the time of collection.	unitless	replicate
Lat	Sample latitude (South is negative).	decimal degrees	lat
Lon	Sample longitude (West is negative)	decimal degrees	lon
Month	Sample month (numeric month)	unitless	month
Year	Sample year in format yyyy.	unitless	year
Species	Species identified. Pocillopora in Moâ€™orea form a species complex that is morphologically indistinguishable, while these were most similar to Pocillopora meandrina, they are indicated as Pocillopora sp.	unitless	taxon
Description	Type of data (all are environmental metagenomes)	unitless	sample_descrip
Sample_ID	Unique sample identifier consistent within the study.	unitless	sample

Status message

Database

Contribute Data

Dataset: Metagenome of Bleached and Non-bleached corals