Dataset: Sea star specimen information: California Academy of Sciences
Deployment: SeaStarMicrobiology_Hewson

Sea star specimen information from the California Academy of Sciences

View Data: For data, See Dataset Metadata Page: https://www.bco-dmo.org/dataset/719932

Principal Investigator:

Ian Hewson (Cornell University, Cornell)

Contact:

Ian Hewson (Cornell University, Cornell)

BCO-DMO Data Manager:

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

Project:

Microbial ecology of sea star wasting disease (Sea Star Microbiology)

Version:

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Description

Note: This dataset was submitted to BCO-DMO and is in the process of being served.

This dataset includes sea star specimen information from the California Academy of Sciences. The specimens described in this dataset were used in a survey of historical sea star-associated densovirus (SSaDV) presence and genome variation.

Methods & Sampling

Dataset acquisition description

Methodology: A survey of historical SSaDV presence and genome variation was performed on specimens donated by the LA County Museum of Natural History and the California Academy of Sciences.

Sampling and analytical procedures: SSaDV was detected using primers/probes targeting two genes on its genome in historical samples from 1942 to present (Hewson et al., 2014). We sought to extend this survey with additional specimens donated from the California Academy of Sciences (SF) and the LA County of Natural History, and to study genome variation in SSaDV by full-length genome sequencing. Donated samples were sampled at the museums by clipping 5 tube feet from each ethanol-preserved sample and placing these into sterile 1.5 ml cryovials. The samples were then returned to the lab at Cornell University for processing.

SSaDV abundance/load will be determined by qPCR following the approach of Hewson et al., 2014 (PNAS). Genome variation will be studied by applying PCR to qPCR positive samples to amplify overlapping parts of the SSaDV genome and then studying their direct sequence-sequence variation.

Data Processing Description

Dataset Processing Description

BCO-DMO Data Manager Processing Notes:
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions
* removed quotation marks around ship names due to character restrictions
* commas changed to semicolons in text fields of data to support csv versions of the data.
* version 2018-02-21 replaces version 2017-10-06 with the only change being that a blank column with parameter "Coord" was removed.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1537111	NSF Division of Ocean Sciences

Instruments

None available yet

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
CatNum	Identifier for the specimen in the catalog	unitless	sample_descrip
Hewson_Lab_Z_Num	Identifier for the sample taken from the specimen used in the Hewson lab	unitless	sample
Size	Size of the specimen (both numeric and descriptive). Numeric values are in cm.	various	length
AccNum	California Academy of Sciences Accession Number	unitless	sample_descrip
AccAcro	California Academy of Sciences Accession Acronym	unitless	sample_descrip
Phylum	Specimen phylum	unitless	taxon
Family	Specimen family	unitless	taxon
HigherClassif	Specimen taxanomic information	unitless	taxon
Genus	Specimen genus	unitless	taxon
Species	Specimen species	unitless	taxon
Author	Author of the species description	unitless	sample_descrip
Locality	Specimen collection location	unitless	site
BegDepth	Start of specimen collection depth range	various	depth
EndDepth	End of specimen collection depth range	various	depth
DepthUnits	Units of beginning and end depth	various	depth
Intertidal	Location description indicating whether the collection site was intertidal (TRUE or FALSE)	unitless	site_descrip
Substratum	Description of sample location substratum	unitless	site_descrip
CollName	Collection the specimen belongs to	unitless	sample_descrip
CollDate	Date of organism accession to collection	date	sample_descrip
Identifier	Person who made the identification	unitless	sample_descrip
IdDate	Date of the identification	date	sample_descrip
OrigFix	Original preservative used to fix the specimen	unitless	sample_descrip
Preservative	Preservative used for long-term preservation	unitless	sample_descrip
Photos	Denotes whether photos are available	unitless	sample_descrip
FieldNum	Specimen number designated by field collector	unitless	sample_descrip
NumSpecimens	Number of specimens in collection	unitless	sample_descrip
ExpeditionName	Expedition name that collected the specimen	unitless	cruise_id
GenBankNum	Genbank accession number for genetic work	unitless	accession_number
CollectMethod	Method of collection	unitless	sample_descrip
Collector	Name of collector or vessel	unitless	sample_descrip
CollDateText	Date of collection	date	sample_descrip
IdDateText	Date of identification	date	date
BegDepthMeters	Beginning depth of collection	meters	depth
EndDepthMeters	Ending depth of collection	meters	depth
BLatDeg	Beginning latitude degrees	degrees	site_descrip
BLatMin	Beginning latitude minutes	minutes	site_descrip
BLatSec	Beginning latitude seconds	seconds	site_descrip
LatHemi	Latitude hemisphere (N = north or S = south)	unitless	site_descrip
ELatDeg	Ending latitude degrees	degrees	site_descrip
ELatMin	Ending latitude minutes	minutes	site_descrip
ELatSec	Ending latitude seconds	seconds	site_descrip
BLongDeg	Beginning longitude degrees	degrees	site_descrip
BLongMin	Beginning longitude minutes	minutes	site_descrip
BLongSec	Beginning longitude seconds	seconds	site_descrip
LongHemi	Longitude hemisphere (W = west or E = east)	unitless	site_descrip
ELongDeg	Ending longitude degrees	degrees	site_descrip
ELongMin	Ending longitude minutes	minutes	site_descrip
ELongSec	Ending longitude seconds	seconds	site_descrip
BegLat	Start of specimen collection latitude range	decimal degrees	lat
EndLat	End of specimen collection latitude range	decimal degrees	lat
BegLong	Start of specimen collection longitude range	decimal degrees	lon
EndLong	End of specimen collection longitude range	decimal degrees	lon

Database

Contribute Data

Dataset: Sea star specimen information: California Academy of Sciences
Deployment: SeaStarMicrobiology_Hewson

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Sea star specimen information: California Academy of SciencesDeployment: SeaStarMicrobiology_Hewson

Dataset acquisition description

Dataset Processing Description

Dataset: Sea star specimen information: California Academy of Sciences
Deployment: SeaStarMicrobiology_Hewson