Dataset: Salp genome and transcriptome
Deployment: UM-08-09

Antarctic salp genome and RNAseq transcriptome

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)

Project:

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

Data URL:

https://osprey.bco-dmo.org/dataset-deployment/675049/data

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Description

This dataset reports Salpa thompsoni specimens used for genomics/transcriptomics with their GenBank accession links.

Related Dataset: Salp sample log: www.bco-dmo.org/dataset/672600

Methods & Sampling

Dataset acquisition description

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

Dataset 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 deployment identifiers
- removed SRA accessions from data display

More information about this dataset deployment

Funding

Award Number	Funding Source
ANT-1044982	NSF Antarctic Sciences

Instruments

Automated DNA Sequencer

Supplied Name: Multiple sequencing platforms: Ion Torrent Proton (Life Technologies, Grand Island, NY), a 454 FLX WGS (Roche Applied Science, Branford, CT), and an Illumina HiSeq 200 (Illumina, San Diego, CA)

Supplied Description:

For genome sequencing

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.

Bioanalyzer

Supplied Name: Agilent 2100 Bioanalyzer

Supplied Description:

For RNA quality control, and to assess the size distribution of library fragments.

Instrument Type

Generic Name: Bioanalyzer

Generic Description:

A Bioanalyzer is a laboratory instrument that provides the sizing and quantification of DNA, RNA, and proteins. One example is the Agilent Bioanalyzer 2100.

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).

Thermal Cycler

Supplied Name:

Supplied Description:

A PCR product ∼500 bp was generated, followed by development of internal primers to produce a smaller PCR product amenable to qPCR.

Instrument Type

Generic Name: Thermal Cycler

Generic Description:

A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
specimen	salp specimen identifier	unitless	sample
cruise_id	cruise identifier	unitless	cruise_id
station	station number	unitless	station
length	salp length	millimeters	length
BioSample_accession	GenBank BioSample accession number	unitless	accession_number
BioSample_accession_link	GenBank BioSample accession number with link to GenBank page	unitless	external_link
SRA_accession	GenBank SRA accession number	unitless	accession_number
SRA_accession_link	GenBank SRA accession number with link to GenBank page	unitless	external_link

Database

Contribute Data

Dataset: Salp genome and transcriptome
Deployment: UM-08-09

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Salp genome and transcriptomeDeployment: UM-08-09

Dataset acquisition description

Dataset Processing Description

Dataset: Salp genome and transcriptome
Deployment: UM-08-09