http://lod.bco-dmo.org/id/dataset/733748
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
2018-04-19
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Assembled metagenomes collected in the Eastern Tropical North Pacific Oxygen Deficient Zone in April 2012 from R/V Thomas G. Thompson cruise TN278
2018-04-19
publication
2018-04-19
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-08-25
publication
https://doi.org/10.26008/1912/bco-dmo.733748.1
Gabrielle Rocap
University of Washington
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: Rocap, G. (2022) Assembled metagenomes collected in the Eastern Tropical North Pacific Oxygen Deficient Zone in April 2012 from R/V Thomas G. Thompson cruise TN278. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-04-19 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.733748.1 [access date]
Assembled metagenomes collected in the Eastern Tropical North Pacific Oxygen Deficient Zone in April 2012 on TN278 Dataset Description: <p>Assembled metagenomes collected in the Eastern Tropical North Pacific Oxygen Deficient Zone in April 2012 on cruise TN278.</p>
<p>These data were published in (Fuchsman et al., 2017)</p> Methods and Sampling: <p>The GenBank BioProject accession number for this data is PRJNA350692. All samples were obtained from station 136 (106.543W, 17.043N; cast 136) or station BB2 (107.148W, 16.527N; cast 141) on cruise TN278 between April 8-9 2012.</p>
<p>Water from all samples was obtained from Niskin bottles on the CTD Rosette. At station 136 we sampled 10 depths including the oxycline and anoxic zones. Two liters of Niskin water were vacuum filtered onto a 0.2 µm SUPOR filter. At station BB2, a nearby station approximately four liters from 100m, 120m, and 150m were each prefiltered through &gt;30 µm filters and subsequently filtered onto 0.2 µm SUPOR filters. All filters were stored at -80C until further processing on shore. The GenBank BioSample accession numbers are SAMN05944799-SAMN05944812.</p>
<p>DNA was extracted from filters using freeze thaw followed by incubation with lysozyme and proteinase K and phenol/chloroform extraction. A Rubicon THRUPLEX kit was used for library prep using 50 ng of DNA per sample. Four libraries were sequenced on an Illumina HiSeq 2500 in rapid mode (25 million 150 bp paired-end reads per sample) at Michigan State. The other 10 libraries were sequenced on an Illumina HiSeq 2500 in high output mode (40-70 million 125 bp paired-end reads per sample) at the University of Utah. Sequences were quality checked, trimmed, and remaining adapter sequences were removed using Trimmomatic (Bolger et al., 2014). Paired reads that overlapped were combined with Flash (Magoc and Salzberg, 2011). FASTQ files of the raw sequence reads are deposited in the Sequence Read Archive under study SRP092212 and the individual file accession numbers SRS1765745-SRS1765758.</p>
<p>Metagenomic sequences from each sample were assembled independently into larger contigs using two approaches. They have been deposited in the Whole Genome Shotgun archive under the accession numbers:<br />
MOXS00000000<br />
MPLT00000000<br />
MPLU00000000<br />
MPLV00000000<br />
MPLW00000000<br />
MPLX00000000<br />
MPLY00000000<br />
MPLZ00000000<br />
MPLZ00000000<br />
MPMB00000000<br />
MPMC00000000<br />
MPMD00000000<br />
MPME00000000<br />
MPMF00000000</p>
<p>First, for de novo assembly we pre-processed reads with the khmer software package (Crusoe et al. 2015), first using normalize-by-median which implements a Digital normalization algorithm (Brown et al., 2012) to reduce high coverage reads to 20x, followed by filter-abund.py to trim reads of kmers with an abundance below 2, and finally we used filter-below-abund.py to trim kmers with counts above 50 (Zhang et al. 2015). We assembled the khmer processed reads with the VELVET (1.2.10) assembler (Zerbino, 2010), using a kmer size of 45. Velvet assemblies have been released as version 1 in Whole Genome Shotgun archive (accession numbers XXXX01000000).</p>
<p>Second, we also generated a second independent de-novo assembly for each sample using MEGAHIT v1.1.2 (Li et al., 2015) in paired end mode with a minimum contig length of 500. MEGAHIT assemblies have been released as version 2 in the Whole Genome Shotgun archive (accession numbers XXXX02000000).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1138368 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1138368
completed
Gabrielle Rocap
University of Washington
206-685-9994
School of Oceanography Box 357940
Seattle
WA
98195
USA
rocap@ocean.washington.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Cruise
Station
CTD_cast
Lat
Long
Date
Depth
Water_Volume
Sample_Name
BioProject_Accession
BioSample_Accession_Number
Short_Read_Archive_Accession_Number
Whole_Genome_Shotgun_Accession_Number
WGS_Velvet_Assembly
WGS_MEGAHIT_Assembly
Sample_Processing
Illumina HiSeq 2500
theme
None, User defined
Cruise identfier
station
cast
latitude
longitude
date
depth
sample_volume
sample identification
accession number
sample description
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Niskin bottle
instrument
BCO-DMO Standard Instruments
TN278
service
Deployment Activity
Eastern Tropical North Pacific Oxygen Deficient Zone
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.
EAGER: Harnessing the power of short-read technology to investigate unexplored microbial communities in the deep euphotic zone
https://osprey.bco-dmo.org/project/725236
EAGER: Harnessing the power of short-read technology to investigate unexplored microbial communities in the deep euphotic zone
<p><em>Extracted from the NSF award abstract:</em></p>
<p>Recent advances in genome sequencing have transformed marine microbial ecology. Metagenomic datasets have led to the discovery of new protein families, underscored the importance of the rare biosphere and even allowed the study of intra-population diversity of dominant members of the community such as Prochlorococcus. Although open ocean microbial communities have been repeatedly demonstrated to vary significantly with depth, in terms of both phylogenetic diversity and biogeochemical function, the vast majority of sequence available in public databases is from surface waters. Much less is known about microbial communities below the surface of the ocean, even those at 50-200m. Next generation sequencing technologies offer a dramatic reduction in cost per base compared to Sanger or even pyrosequencing approaches. The very short read lengths from these platforms have not yet been successfully applied to mixed communities. This project is a metagenomic study of the microbial communities throughout the water column in the South Atlantic gyre using the ABI SOLiD platform with the following objectives:</p>
<p>- Construct and sequence paired-end metagenomic libraries from the surface, chlorophyll maximum, deep euphotic zone and twilight zone in the South Atlantic gyre using ABI SOLiD technology.</p>
<p>- Apply information theory based software methods to assemble the short read sequences and reconstruct the phylogenetic diversity and metabolic potential of these communities.</p>
<p>- Compare reconstructed sequences to existing metagenomic data from other parts of the world's oceans and to metaproteomic data from the the same location to inform sampling strategies and methodological choices for a proposed global molecular oceanic survey (Biogeotraces). </p>
<p>This project is appropriate as an EAGER because the genomic potential of deep euphotic zone and twilight zone communities will be very different from those in surface waters. Thus, this dataset will reshape our understanding of oligotrophic community function. Second, the massive advance in data generated at a low cost by short-read sequencing platforms has the potential to transform microbial oceanography by allowing metagenomic analyses to be routinely employed in hypothesis-driven experiments. However, new interdisciplinary tools are required to assemble and interpret this data. Until these next generation bioinformatic methods are established, proposals that take advantage of these technological breakthroughs remain high risk.</p>
<p>Broader Impacts: Metagenomic analyses of microbial communities collected on a GEOTRACES compliant cruise in the South Atlantic will provide a pilot dataset demonstrating the potential of short-read sequencing technologies for a future sectional molecular survey program. A post-doctoral researcher and a graduate student will be trained in the interdisciplinary perspectives required to analyze this sequence data and interpret it in a biogeochemical context.</p>
EAGER Deep Prochlorococcus
largerWorkCitation
project
eng; USA
biota
oceans
Eastern Tropical North Pacific Oxygen Deficient Zone
-107.148
-106.543
16.527
17.043
2012-04-08
2012-04-09
South Atlantic, Eastern Tropical North Pacific
0
BCO-DMO catalogue of parameters from Assembled metagenomes collected in the Eastern Tropical North Pacific Oxygen Deficient Zone in April 2012 from R/V Thomas G. Thompson cruise TN278
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/733975.rdf
Name: Cruise
Units: unitless
Description: <p>Cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/733976.rdf
Name: Station
Units: unitless
Description: <p>Station identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/733977.rdf
Name: CTD_cast
Units: unitless
Description: <p>CTD cast number</p>
http://lod.bco-dmo.org/id/dataset-parameter/733978.rdf
Name: Lat
Units: decimal degrees
Description: <p>Latitude; positive values = North</p>
http://lod.bco-dmo.org/id/dataset-parameter/733979.rdf
Name: Long
Units: decimal degrees
Description: <p>Longitude; positive values = East</p>
http://lod.bco-dmo.org/id/dataset-parameter/733980.rdf
Name: Date
Units: unitless
Description: <p>Date of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/733981.rdf
Name: Depth
Units: meters (m)
Description: <p>Depth of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/733982.rdf
Name: Water_Volume
Units: liters (L)
Description: <p>Water volume collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/733983.rdf
Name: Sample_Name
Units: unitless
Description: <p>Sample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/733984.rdf
Name: BioProject_Accession
Units: unitless
Description: <p>NCBI BioProject accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/733985.rdf
Name: BioSample_Accession_Number
Units: unitless
Description: <p>NCBI BioSample accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/733986.rdf
Name: Short_Read_Archive_Accession_Number
Units: unitless
Description: <p>NCBI Short Read Archive (SRA) accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/733987.rdf
Name: Whole_Genome_Shotgun_Accession_Number
Units: unitless
Description: <p>Whole Genome Shotgun accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/733988.rdf
Name: WGS_Velvet_Assembly
Units: unitless
Description: <p>WGS Velvet Assembly</p>
http://lod.bco-dmo.org/id/dataset-parameter/733989.rdf
Name: WGS_MEGAHIT_Assembly
Units: unitless
Description: <p>WGS MEGAHIT Assembly</p>
http://lod.bco-dmo.org/id/dataset-parameter/733990.rdf
Name: Sample_Processing
Units: unitless
Description: <p>Description of sample processing</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
7121
https://darchive.mblwhoilibrary.org/bitstream/1912/29270/1/dataset-733748_etnp-odz-metagenomes-april-2012__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.733748.1
download
onLine
dataset
<p>The GenBank BioProject accession number for this data is PRJNA350692. All samples were obtained from station 136 (106.543W, 17.043N; cast 136) or station BB2 (107.148W, 16.527N; cast 141) on cruise TN278 between April 8-9 2012.</p>
<p>Water from all samples was obtained from Niskin bottles on the CTD Rosette. At station 136 we sampled 10 depths including the oxycline and anoxic zones. Two liters of Niskin water were vacuum filtered onto a 0.2 µm SUPOR filter. At station BB2, a nearby station approximately four liters from 100m, 120m, and 150m were each prefiltered through &gt;30 µm filters and subsequently filtered onto 0.2 µm SUPOR filters. All filters were stored at -80C until further processing on shore. The GenBank BioSample accession numbers are SAMN05944799-SAMN05944812.</p>
<p>DNA was extracted from filters using freeze thaw followed by incubation with lysozyme and proteinase K and phenol/chloroform extraction. A Rubicon THRUPLEX kit was used for library prep using 50 ng of DNA per sample. Four libraries were sequenced on an Illumina HiSeq 2500 in rapid mode (25 million 150 bp paired-end reads per sample) at Michigan State. The other 10 libraries were sequenced on an Illumina HiSeq 2500 in high output mode (40-70 million 125 bp paired-end reads per sample) at the University of Utah. Sequences were quality checked, trimmed, and remaining adapter sequences were removed using Trimmomatic (Bolger et al., 2014). Paired reads that overlapped were combined with Flash (Magoc and Salzberg, 2011). FASTQ files of the raw sequence reads are deposited in the Sequence Read Archive under study SRP092212 and the individual file accession numbers SRS1765745-SRS1765758.</p>
<p>Metagenomic sequences from each sample were assembled independently into larger contigs using two approaches. They have been deposited in the Whole Genome Shotgun archive under the accession numbers:<br />
MOXS00000000<br />
MPLT00000000<br />
MPLU00000000<br />
MPLV00000000<br />
MPLW00000000<br />
MPLX00000000<br />
MPLY00000000<br />
MPLZ00000000<br />
MPLZ00000000<br />
MPMB00000000<br />
MPMC00000000<br />
MPMD00000000<br />
MPME00000000<br />
MPMF00000000</p>
<p>First, for de novo assembly we pre-processed reads with the khmer software package (Crusoe et al. 2015), first using normalize-by-median which implements a Digital normalization algorithm (Brown et al., 2012) to reduce high coverage reads to 20x, followed by filter-abund.py to trim reads of kmers with an abundance below 2, and finally we used filter-below-abund.py to trim kmers with counts above 50 (Zhang et al. 2015). We assembled the khmer processed reads with the VELVET (1.2.10) assembler (Zerbino, 2010), using a kmer size of 45. Velvet assemblies have been released as version 1 in Whole Genome Shotgun archive (accession numbers XXXX01000000).</p>
<p>Second, we also generated a second independent de-novo assembly for each sample using MEGAHIT v1.1.2 (Li et al., 2015) in paired end mode with a minimum contig length of 500. MEGAHIT assemblies have been released as version 2 in the Whole Genome Shotgun archive (accession numbers XXXX02000000).</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Processing:<br />
-modified parameter names to conform with BCO-DMO naming conventions (replaced spaces with underscores);<br />
-added URLs linking to NCBI;<br />
-split original "Lat Long" column into two separate columns; removed trailing "N" and "W" and removed degrees sign; changed lon to negative values;<br />
-formatted date to yyyy-mm-dd from dd-APR-yyyy;<br />
-removed "m" (units) from Depth column values and "L" from Water_Volume column.</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
Illumina HiSeq 2500
Illumina HiSeq 2500
PI Supplied Instrument Name: Illumina HiSeq 2500 PI Supplied Instrument Description:Libraries were sequenced on an Illumina HiSeq 2500. Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
PI Supplied Instrument Name: PI Supplied Instrument Description:Water from all samples was obtained from Niskin bottles on the CTD Rosette. Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Cruise: TN278
TN278
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN278
Allan Devol
University of Washington
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel