Dataset: Salp sample log

Name: Salp specimen log for genomic and transcriptomic study collected from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2 in the Southern Ocean from 2009-2011 (Salp_Antarctic project)
Published: 2017-01-06
Keywords: Salpa thompsoni, environmental transcriptomics, RNAseq, genome sequence, Thaliacea, miRNA, biota, oceans

Cite This Dataset

DOI:10.1575/1912/bco-dmo.728220

Spatial Extent: N:-60.901 E:42.002 S:-66.183 W:-74.567

Temporal Extent: 2009-01-12 - 2011-12-02

Project:

Population ecology of Salpa thompsoni based on molecular indicators (Salp_Antarctic)

Chief Scientist:

Ann Bucklin (University of Connecticut, UConn - Avery Point)

Principal Investigator:

Ann Bucklin (University of Connecticut, UConn - Avery Point)

Co-Principal Investigator:

Rachel J. O'Neill (University of Connecticut, UConn)

Diana Payne (Connecticut Sea Grant, CTSG)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version Date:

2017-01-06

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Salp specimen log for genomic and transcriptomic study collected from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2 in the Southern Ocean from 2009-2011 (Salp_Antarctic project)

Expand/Collapse All

Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2017-01-06	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.1575/1912/bco-dmo.728220	2018-02-23

Description

This dataset is a log of the Salpa thompsoni specimens used for genomics/transcriptomics. Reported parameters include cruise id, region, season and area, location, number of samples collected, temperature, salinity, depth range of the samples, and the depth of the water at the collection site.

Related Dataset: Salp genome and transcriptome

Methods & Sampling

1) Cruise R/V LM GOULD (LMG1110): Samples collected using Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS) with a mouth opening of 1-m2 and nine 335μm mesh nets; upper 200 m were sampled with a 2.3 m2 Isaacs-Kidd Midwater Trawl (IKMT) with a 505 µm mesh net. Western Antarctic Peninsula region, Southern Ocean (November-December 2011)

2) Cruise R/V Polarstern (PS-ANT-XVII/2): Samples collected using a Rectangular Midwater Trawl (RMT 1+8) from the upper 200 m. Western Antarctic Peninsula region, Southern Ocean (January 2011)

3) Cruise R/V Umitaka Maru (UM-08-09): Samples collected using a RMT 1+8 from 2,000 m to surface. Indian Sector, Southern Ocean (January 2009)

Data Processing Description

Molecular genetic (genomic and transcriptomic) data resulting from this project have been submitted to appropriate sections of the NCBI GenBank database, as follows:

The Salpa thompsoni Whole Genome Shotgun project (see Jue et al., 2016) has been deposited at DDBJ/ENA/GenBank Genome section under the Accession No. MKHR00000000. The version described in this paper is version MKHR01000000. The genomic data include the final assembly and annotations, as well as all of the raw data files (genomic and small RNAs). Accession Nos. are assigned to the genomic data submission, as follows: SUBID, SUB1479239; BioProject, PRJNA318929; BioSample, SAMN04870323. The Salp Genome Bioproject information and data are available at https://www.ncbi.nlm.nih.gov/genome/?term=MKHR00000000.

The Salpa thompsoni Transcriptome Shotgun Assembly project (see Batta-Lona et al., 2016) has been deposited at DDBJ/ENA/GenBank under the Accession No. GFCC00000000. The version described in this paper is version GFCC01000000. The transcriptomic data includes raw sequencing data and alignment information. The Bioproject Accession No. is PRJNA279245, which includes RNA-seq data from 48 field-collected specimens, which are assigned Biosample Accession Nos. SAMN05604989 - SAMN05605036. The Salp Transcriptome Bioproject information and data are available at https://www.ncbi.nlm.nih.gov/nuccore/GFCC00000000.

BCO-DMO Processing notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- added cruise_id column
- replaced spaces with underscores

Data Files

File
salp_sample_log.csv (Comma Separated Values (.csv), 916 bytes) MD5:976908c0d3dfdff9a5bfefb3e6ffd5a9 Primary data file for dataset ID 672600

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Antarctic Sciences	ANT-1044982

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
ANT-XXVII-2	PS77	2010-11-28	R/V Polarstern	Eberhard Fahrbach (Chief Scientist)	data info
LMG1110		2011-11-02	ARSV Laurence M. Gould	Ann Bucklin (Chief Scientist)	data info
UM-08-09		2009-01-12	Umitaka-Maru		data info

Instruments

Isaacs-Kidd Midwater Trawl

Supplied Name: 2.3 m2 Isaacs-Kidd Midwater Trawl (IKMT) with a 505 µm mesh net

Supplied Description:

Instrument Type

Generic Name: Isaacs-Kidd Midwater Trawl

Acronym: IKMT

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/NETT0071/

Generic Description:

A trawl with a pentagonal mouth opening and a dihedral depressor vane as part of the mouth opening. IKMTs come in various dimensions (refer to individual dataset documentation).

The original IKMTs were 10 foot (304 cm) and 15 foot (457 cm) at the mouth. The 10 foot IKMT net was 31 feet (9.45 m) in length (Wiebe and Benfield 2003).

Midwater Trawl

Supplied Name: Rectangular Midwater Trawl (RMT 1+8)

Supplied Description:

Instrument Type

Generic Name: Midwater Trawl

Acronym: TrawlMid

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/23/

Generic Description:

A mid-water or pelagic trawl is a net towed at a chosen depth in the water column to catch schooling fish such as herring and mackerel. Midwater trawl nets have very large front openings to herd schooling fish toward the back end where they become trapped in the narrow "broiler". The sides of the deployed net are spread horizontally with two large metal foils, called "doors," positioned in front of the net. As the trawler moves forward, the doors, and therefore the net, are forced outward, keeping the net open.
This instrument designation is used when specific make and model are not known.

MOCNESS1

Supplied Name: Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS) with a mouth opening of 1-m2 and nine 335μm mesh nets

Supplied Description:

Instrument Type

Generic Name: MOCNESS1

Acronym: MOC1

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/NETT0097/

Generic Description:

The Multiple Opening/Closing Net and Environmental Sensing System or MOCNESS is a family of net systems based on the Tucker Trawl principle. The MOCNESS-1 carries nine 1-m2 nets usually of 335 micrometer mesh and is intended for use with the macrozooplankton. All nets are black to reduce contrast with the background. A motor/toggle release assembly is mounted on the top portion of the frame and stainless steel cables with swaged fittings are used to attach the net bar to the toggle release. A stepping motor in a pressure compensated case filled with oil turns the escapement crankshaft of the toggle release which sequentially releases the nets to an open then closed position on command from the surface. -- from the MOCNESS Operations Manual (1999 + 2003).

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
cruise_id	cruise identifier	unitless	cruise_id
region	region of Southern Ocean	unitless	region
season	season and year of collection	unitless	season
area	area within region of Southern Ocean	unitless	region
station	station number	unitless	station
lat	latitude; north is positive	decimal degrees	lat
lon	longitude; east is positive	decimal degrees	lon
num_samples	number of samples collected	unitless	count
temp	temperature	degrees Celsius	temp
sal	salinity	PPT	sal
depth_range	sampled depth	meters	depth_range
depth_w	water column depth	meters	depth_w

Status message

Database

Contribute Data

Dataset: Salp sample log