Dataset: Hurricane Harvey Coral Gene Expression

Name: Coral gene expression Sequence Read Archive (SRA) accession numbers and information for samples collected at the Flower Garden Banks National Marine Sanctuary in the Gulf of Mexico in September and October of 2017 to capture effects of Hurricane Harvey
Published: 2020-06-30
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.817298.1

Spatial Extent: N:27.908 E:-93.60019 S:27.8819 W:-93.62828

Temporal Extent: 2017-09 - 2017-10

Project:

RAPID: Collaborative Research: Impact of freshwater runoff from Hurricane Harvey on coral reef benthic organisms and associated microbial communities (Rapid Reefs Harvey)

Principal Investigator:

Sarah W. Davies (Boston University, BU)

Contact:

Rachel Wright (Boston University, BU)

BCO-DMO Data Manager:

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

Version:

Version Date:

2020-06-30

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Coral gene expression Sequence Read Archive (SRA) accession numbers and information for samples collected at the Flower Garden Banks National Marine Sanctuary in the Gulf of Mexico in September and October of 2017 to capture effects of Hurricane Harvey

Abstract:

To capture the immediate effects of storm-driven freshwater runoff on coral and symbiont physiology, we leveraged the heavy rainfall associated with Hurricane Harvey in late August 2017 by sampling FGB coral gene expression at two time points: September 2017, when surface water salinity was reduced (∼34 ppt); and 1 month later when salinity had returned to typical levels (∼36 ppt in October 2017). This dataset includes Sequence Read Archive (SRA) and BioSample accessions under BioProject PRJNA552981 at The National Center for Biotechnology Information. It also contains sample information and species names for samples collected the east and west banks of the Flower Garden Banks National Marine Sanctuary (FGBNMS) at 80ft. These data were published in Wright et al. (2019).

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2020-06-30	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.817298.1	2020-07-08

Description

This dataset includes Sequence Read Archive (SRA) and BioSample accessions under BioProject PRJNA552981 at The National Center for Biotechnology Information. It also contains sample information and species names for samples collected the east and west banks of the Flower Garden Banks National Marine Sanctuary (FGBNMS) at 80ft.

These data were published in Wright et al. (2019).

Methods & Sampling

Location:

East and west banks of the Flower Garden Banks National Marine Sanctuary (FGBNMS) 80ft

Sampling Events:
Hurricane Harvey FGB October 2017, Hurricane Harvey FGB October 2018.

Methodology:

Tagseq libraries were prepared and SE 50bp reads were generated using Illumina Hiseq 2500 platform.

Coral tissue samples were preserved midday underwater. RNA was isolated and samples were processed for tagseq profiling.

Data Processing Description

Coral tissue samples were preserved midday underwater. RNA was isolated and samples were processed for tagseq profiling.

BCO-DMO Data Manager Processing Notes:
* Originally submitted Excel file Wright_etal_metadada.xlsx extracted to csv file.
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions (spaces, +, and - changed to underscores). Units in parentheses removed and added to Parameter Description metadata section.
* blank values (originally submitted as NR) in this dataset are displayed as "nd" for "no data." nd is the default missing data identifier in the BCO-DMO system.
* Combined "Lat Lon" column (e.g. "27°52'54.84", 93°37'41.84") separated into separate lat and lon columns in decimal degree format.

Data Files

File
hurr_harvey_sra_samples.csv (Comma Separated Values (.csv), 4.50 KB) MD5:2d62c2041a8d22c37330d36dc8c7c68a Primary data file for dataset ID 817298

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1800904

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: Illumina Hiseq 2500 platform

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
Sample_Name	Sample name	unitless	sample
Time	Sample time in format (Full month name and four digit year)	unitless	Date_Month
Bank	east or west bank of the Flower Garden Banks	unitless	site_descrip
Buoy	Buoy number samples were collected from	unitless	site_descrip
Lat	Sample latitude	decimal degrees	lat
Lon	Sample longitude	decimal degrees	lon
Species	Scientific name (Genus species)	unitless	taxon
Depth	Sample depth	meters (m)	depth
SRA	Sequence Read Archive (SRA) accession number at NCBI	unitless	accession_number
Accession	BioSample accession number at NCBI	unitless	accession_number