Dataset: DHAB halocline - nematodes

Name: Metatranscriptome data for pools of 10 nematodes picked from halocline and nearby control sediments from R/V Atlantis cruise AT18-14 in the Eastern Mediterranean in 2011 (DHAB Metazoans project)
Published: 2015-05-27
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:35.3145 E:21.7052 S:35.2859 W:21.4057

Project:

Investigations into the Physiological State of DHAB Metazoans (DHAB Metazoans)

Principal Investigator:

Joan M. Bernhard (Woods Hole Oceanographic Institution, WHOI)

Co-Principal Investigator:

Virginia P. Edgcomb (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

27 May 2015

Version Date:

2015-05-27

Validated:

Yes

Current State:

Final with updates expected

Data URL:

https://www.bco-dmo.org/dataset/559351/data

Metatranscriptome data for pools of 10 nematodes picked from halocline and nearby control sediments from R/V Atlantis cruise AT18-14 in the Eastern Mediterranean in 2011 (DHAB Metazoans project)

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Description

Metatranscriptome data for pools of 10 nematodes picked from halocline and nearby control sediments; samples collected from the Eastern Mediterranean Deep-sea Hypersaline Anoxic Basins (DHAB) Urania, L’Atalante, Discovery (roughly 35 13N, 21 29 E; depth ~3500 m).

Acquisition Description

Pushcore and scoop samples were collected by ROV Jason. Scoop samples were preserved immediately on the seafloor in RNAlater. Upon retrieval to the ocean surface cores were quickly profiled for oxygen and then subsamples were preserved in RNAlater. Nematodes were picked from whole preserved sediments in the laboratory using a dissection microscope, rinsed 3x in RNAlater, and collected in pools of 10 nematodes for RNA extraction. Metatranscriptome libraries for Illumina sequencing were prepared using 5 micro liters of total RNA and the Ovation 3'DGE System (NuGen) and a Zymo Research Concentrator Kit.

Processing Description

All resulting reads were aligned to the protein database NCBI-Nr for initial screening of prokaryotic contaminants. Raw reads are deposited in the Genbank SRA with Run IDs SRR2038214 (Atalante Control) SRR2038319 (Discovery Control), SRR2038321 (Atlalante Lower Interface, or halo cline), SRR2038320 (Atalante White Zone, or upper halo cline), SRR2038323 (Discovery Upper Interface).

Despite polyA enrichment during cDNA creation, which should enrich for eukaryotic mRNA, the resulting transcriptomic sequences were dominated by bacterial and archaeal sequence reads in most samples (average 60%). Once filtered of contaminant prokaryotic reads, approximately half (average 45%) of the remaining DHAB and Control reads were affiliated to nematode sequences when they were compared to sequences in the nematode-specific transcript database NEMBASE4 (Elsworth, Wasmuth & Blaxter 2011).

BCO-DMO Processing:
- Added latitude and longitude using values previously provided in the "DHAB halocline sediment pyrotags - eukaryotes" dataset.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1061391

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
AT18-14		2011-11-25	R/V Atlantis	Virginia P. Edgcomb (Chief Scientist) Joan M. Bernhard (Principal Investigator)	data info

Instruments

ROV Jason

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.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
sample	Description of sample.	text	sample
lat	Approximate latitude of sampling site.	decimal degrees	lat
lon	Approximate longitude of sampling site.	decimal degrees	lon
cruise_id	Cruise identification number. (AT18-14 = R/V Atlantis cruise number 18-14)	text	cruise_id
BioSample_id	GenBank BioSample identification number.	text	accession_number
SRA_exp_id	GenBank Sequence Read Archive experiment identification.	text	accession_number
SRA_run_id	GenBank Sequence Read Archive run identification.	text	accession_number
BioProject_id	GenBank BioProject identification and hyperlink.	text	accession_number

Database

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Dataset: DHAB halocline - nematodes