Dataset: Vent_CSP_SAG
Deployment: AT15-38

Single amplified genomes (SAGs) of microbial cells isolated from Crab Spa, East Pacific Rise

View Data: For data, See Dataset Metadata Page: https://www.bco-dmo.org/dataset/660802

Principal Investigator:

Dr Ramunas Stepanauskas (Bigelow Laboratory for Ocean Sciences)

BCO-DMO Data Manager:

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

Project:

An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents (Microbial Communities at Deep-Sea Vents)

Current State:

Final no updates expected

Deployment Synonyms:

FIX08B

Version Date:

2016-10-05

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Description

The accession links are not yet public. They will be archived at the Integrated Microbial Genomes (IMG), at the Joint Genome Inst. (JGI), US Dept. of Energy (DOE). Please contact the PI for further details.

Methods & Sampling

Dataset acquisition description

AT15-38: Samples for SAGs were obtained using the so-called 'titanium major samplers' (von Damm et al, 1985). Replicate samples of 1 ml aliquots of water were cryopreserved with 6% glycine betaine (Sigma) or 15% glycerol and stored at -80 ºC for the ”Single Cell” aliquot.

AT26-10: Background samples were obtained from the IGTs, in which the incubations were carried out. Just in this case, an aliquot was removed after sample retrieval and before starting the incubation. During AT26-10, samples were preserved with Gly-TE and stored at -80.

Cells were sorted, identified and sequenced by the Bigelow Laboratory Single Cell Genomics FacilityCenter (SCGC), following SCGCthe facilities’s standard practices: SCGC_Services_Description.pdf

Data Processing Description

Dataset Processing Description

On average, at least 5 million 2x150 bp or longer paired-end reads were generated per SAG using in-house MiSeq and NextSeq (Illumina) instruments. The obtained reads were pre-processed and, de novo, assembled and quality-controlled using algorithms SCGC's standard protocols that are optimized for single cell MDA products . A combination of tetramer homogeneity tests and blast searches against reference databases is used to detect potential DNA contaminants among the assembled contigs. Benchmark data demonstrating SCGC SAG WGS whole genome sequencing pipeline performance is available from the SCGC website http://data.bigelow.org/~scgc/WGS_benchmark_data/.

Genome annotation was performed through IMG (http://img-stage.jgi-psf.org/cgi-bin/submit/main.cgi).

Additional related references (pdf)

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1136488	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name:

Supplied Description:

MiSeq and NextSeq (Illumina) sequencers

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.

Isobaric Gas-Tight Sampler

Supplied Name: IGT

Supplied Description:

Instrument Type

Generic Name: Isobaric Gas-Tight Sampler

Acronym: IGT Sampler

Generic Description:

Isobaric Gas Tight (IGT) samplers, designed and built by scientists and engineers at WHOI, are titanium instruments designed to be used with deep submergence vehicles to sample corrosive hydrothermal vent fluids at high temperature and high pressure. The IGT prevents the sampled fluid from degassing as pressure decreases during the vehicle’s ascent to the surface.

ROV Jason

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: ROV Jason

Generic Description:

The Remotely Operated Vehicle (ROV) Jason is operated by the Deep Submergence Laboratory (DSL) at Woods Hole Oceanographic Institution (WHOI). WHOI engineers and scientists designed and built the ROV Jason to give scientists access to the seafloor that didn't require them leaving the deck of the ship. Jason is a two-body ROV system. A 10-kilometer (6-mile) fiber-optic cable delivers electrical power and commands from the ship through Medea and down to Jason, which then returns data and live video imagery. Medea serves as a shock absorber, buffering Jason from the movements of the ship, while providing lighting and a bird’s eye view of the ROV during seafloor operations. During each dive (deployment of the ROV), Jason pilots and scientists work from a control room on the ship to monitor Jason’s instruments and video while maneuvering the vehicle and optionally performing a variety of sampling activities. Jason is equipped with sonar imagers, water samplers, video and still cameras, and lighting gear. Jason’s manipulator arms collect samples of rock, sediment, or marine life and place them in the vehicle’s basket or on "elevator" platforms that float heavier loads to the surface. More information is available from the operator site at URL. https://ndsf.whoi.edu/jason/

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
taxon_oid	Identification number of the Single Amplified Genome (SAG) in IMG	unitless	taxon_code
SAG_id	The identifier of the SAG	unitless	sample
taxon	Taxonomic affiliation of the SAG	unitless	taxon
source	The origin of the sample used for the single cell sorting: Background: Cell sorted from the natural water samples Control: Cell sorted from the natural water samples incubated in isobaric chambers without any amendments NO3-/H2, ~24C: Cell sorted from the natural water samples incubated at 24oC in isobaric chambers with the addition of NO3- (nitrate) and hydrogen (H2) H2 only: Cell sorted from the natural water samples incubated at 24oC in isobaric chambers with the addition of hydrogen (H2) NO3- only: Cell sorted from the natural water samples incubated at 24oC in isobaric chambers with the addition of NO3- (nitrate)hydrogen (H2) O2, ~110uM: Cell sorted from the natural water samples incubated at 24oC in isobaric chambers with the addition of 110uM of O2 (oxygen) NO3-/H2, ~50C: Cell sorted from the natural water samples incubated at 50oC in isobaric chambers with the addition of NO3- (nitrate) and hydrogen (H2)	unitless	treatment
deployment	J denotes "Jason dive" followed by the nember of dive	unitless	dive_id
accession_IMG	The accession number in IMG	unitless	accession_number
GOLD_Analysis_project_id	The project identification number in the GOLD Database; accession number for the metadata	unitless	accession_number
GOLD_sequencing_strategy	The strategy used for sequencing (whole genome sequencing vs amplicon sequencing)	unitless	sampling_method
latitude	Latitude of the sampling site	unitless	lat
longitude	Longitude of the sampling site	unitless	lon
assembly_size	The total size of the assembled contigs	base pairs (bp)	no_bcodmo_term
gene_count	Number of identified genes	unitless	count
accession_link	Link to taxon_oid at IMG database	unitless	external_link
study_name	The name of the study	unitless	exp_id
site	location where samples were collected	unitless	site
sequencing_center	the name of the center where the samples were sequenced	unitless	site
date_collect	date the samples were collected; formatted as month\day\year	unitless	date

Database

Contribute Data

Dataset: Vent_CSP_SAGDeployment: AT15-38

Dataset acquisition description

Dataset Processing Description

Dataset: Vent_CSP_SAG
Deployment: AT15-38