http://lod.bco-dmo.org/id/dataset/559351
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2015-05-27
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
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)
2015-05-27
publication
2015-05-27
revision
BCO-DMO Linked Data URI
2015-05-27
creation
http://lod.bco-dmo.org/id/dataset/559351
Joan M. Bernhard
Woods Hole Oceanographic Institution
principalInvestigator
Virginia P. Edgcomb
Woods Hole Oceanographic Institution
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Bernhard, J. M., Edgcomb, V. P. (2015) 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). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 27 May 2015) Version Date 2015-05-27 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/559351 [access date]
Metatranscriptome data for pools of 10 nematodes picked from halocline and nearby control sediments. Dataset Description: <p>Metatranscriptome data for pools of 10 nematodes picked from halocline and nearby control sediments; samples collected from the&nbsp; Eastern Mediterranean Deep-sea Hypersaline Anoxic Basins (DHAB) Urania, L’Atalante, Discovery (roughly 35 13N, 21 29 E; depth ~3500 m).</p> Methods and Sampling: <p>Pushcore and scoop samples were collected by ROV <em>Jason. </em>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.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1061391 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1061391
onGoing
Joan M. Bernhard
Woods Hole Oceanographic Institution
508-289-3480
Department of Geology and Geophysics Woods Hole Oceanographic Institution, MS#52
Woods Hole
MA
02543
USA
jbernhard@whoi.edu
pointOfContact
Virginia P. Edgcomb
Woods Hole Oceanographic Institution
508-289-3734
Department of Geology and Geophysics 220 McLean Lab, MS #8
Woods Hole
MA
02543
USA
vedgcomb@whoi.edu
pointOfContact
asNeeded
Dataset Version: 27 May 2015
Unknown
sample
lat
lon
cruise_id
BioSample_id
SRA_exp_id
SRA_run_id
BioProject_id
ROV Jason
theme
None, User defined
sample identification
latitude
longitude
Cruise identfier
accession number
featureType
BCO-DMO Standard Parameters
ROV Jason
instrument
BCO-DMO Standard Instruments
AT18-14
service
Deployment Activity
Eastern Mediterranean; 35.3 N 21.7 E
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Investigations into the Physiological State of DHAB Metazoans
https://osprey.bco-dmo.org/project/2177
Investigations into the Physiological State of DHAB Metazoans
<p>Invasion of the Body Snatchers!</p>
<p>Description text from the NSF award abstract:<br />
Although it has been known for many decades that metazoans inhabit anoxic habitats either on a periodic, transient, or semi permanent basis, none have been shown to complete an entire life cycle without access to oxygen. The remarkable recent observation that loriciferan metazoans complete a full life cycle without access to dissolved oxygen raises questions in the fields of physiology and evolution. The habitat from which the anaerobic animals were collected is sediment from a Deep Hypersaline Anoxic Brine (DHAB) in the eastern Mediterranean Sea at a water depth greater than 3 kilometers. DHABs are one of the most extreme marine environments known to science, with a water chemistry considered anathema to eukaryotic life. While the possibility of anaerobic metazoa is exciting, there are other potential explanations that warrant investigation before biology textbooks are rewritten. One alternative scenario is that remnant metazoa bodies were inhabited by anaerobic bacteria and/or archaea.</p>
<p>The overall goal of this project is to determine if the dominant loriciferan and nematode taxon in each of three DHABs represent living populations. Because remnant DNA can be preserved in anoxic settings for long periods of time, the project will include in situ preservation for RNA analysis. Further, because there is also some chance of RNA preservation in these anoxic sedimentary environments, the study will include analyses of the more ephemeral mRNA and also Transmission Electron Microscopy (TEM). On three ship days added to a funded cruise to sample DHABs for other purposes, an ROV will be used to preserve samples in situ. The specific aims are to: (1) Use RNA and DNA analysis to establish if metazoan ribosomal RNA and functional genes were active at the time of in situ preservation in the dominant two metazoan taxa from each DHAB. (2) Identify the prokaryotes associated with DHAB metazoans using RNA analysis and FISH/CARD FISH. (3) Assess the state of cellular ultrastructure in metazoans using TEM to determine the state of organelles (e.g., nuclei, Golgi, hydrogenosomes) and if DHAB metazoans have specialized cellular structures.</p>
<p>Regardless of results, significant information will be obtained. If the metazoans are not living in the DHABs, then a paradigm shift is unnecessary and physiology text books do not need to be rewritten. If the metazoans are living in the DHAB, then a paradigm shift is required.<br />
</p>
DHAB Metazoans
largerWorkCitation
project
eng; USA
biota
oceans
Eastern Mediterranean; 35.3 N 21.7 E
2015-05-27
Eastern Mediterranean; 35.3 N, 21.7 E
0
BCO-DMO catalogue of parameters from 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)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/559360.rdf
Name: sample
Units: text
Description: <p>Description of sample.</p>
http://lod.bco-dmo.org/id/dataset-parameter/559361.rdf
Name: lat
Units: decimal degrees
Description: <p>Approximate latitude of sampling site.</p>
http://lod.bco-dmo.org/id/dataset-parameter/559362.rdf
Name: lon
Units: decimal degrees
Description: <p>Approximate longitude of sampling site.</p>
http://lod.bco-dmo.org/id/dataset-parameter/559363.rdf
Name: cruise_id
Units: text
Description: <p>Cruise identification number. (AT18-14 = R/V Atlantis cruise number 18-14)</p>
http://lod.bco-dmo.org/id/dataset-parameter/559364.rdf
Name: BioSample_id
Units: text
Description: <p>GenBank BioSample identification number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/559365.rdf
Name: SRA_exp_id
Units: text
Description: <p>GenBank Sequence Read Archive experiment identification.</p>
http://lod.bco-dmo.org/id/dataset-parameter/559366.rdf
Name: SRA_run_id
Units: text
Description: <p>GenBank Sequence Read Archive run identification.</p>
http://lod.bco-dmo.org/id/dataset-parameter/559367.rdf
Name: BioProject_id
Units: text
Description: <p>GenBank BioProject identification and hyperlink.</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
928
https://datadocs.bco-dmo.org/file/0AAMn1oCkBlGDB/DHAB_nematodes.csv
DHAB_nematodes.csv
Primary data file for dataset ID 559351
download
https://osprey.bco-dmo.org/dataset/559351/data/download
download
onLine
dataset
<p>Pushcore and scoop samples were collected by ROV <em>Jason. </em>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.</p>
Specified by the Principal Investigator(s)
<p>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).</p>
<p>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 &amp; Blaxter 2011).</p>
<p>BCO-DMO Processing:<br />
- Added latitude and longitude using values previously provided in the "<a href="http://www.bco-dmo.org/dataset/553959" target="_blank">DHAB halocline sediment pyrotags - eukaryotes</a>" dataset.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
ROV Jason
ROV Jason
PI Supplied Instrument Name: ROV Jason Instrument Name: ROV Jason Instrument Short Name:ROV Jason Instrument 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/
Cruise: AT18-14
AT18-14
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT18-14
Virginia P. Edgcomb
Woods Hole Oceanographic Institution
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel