http://lod.bco-dmo.org/id/dataset/626150
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
2015-11-05
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Sub-seafloor metatranscriptomes from anaerobic Peru Margin sediments collected on R/V JOIDES Resolution Leg 201 in 2002
2015-11-05
publication
2015-11-05
revision
BCO-DMO Linked Data URI
2015-11-05
creation
http://lod.bco-dmo.org/id/dataset/626150
William D. Orsi
Woods Hole Oceanographic Institution
principalInvestigator
Jennifer F. Biddle
University of Delaware
principalInvestigator
Glenn D. Christman
University of Delaware
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: Orsi, W. D., Edgcomb, V. P., Christman, G. D., Biddle, J. F. (2015) Sub-seafloor metatranscriptomes from anaerobic Peru Margin sediments collected on R/V JOIDES Resolution Leg 201 in 2002. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 05 November 2015) Version Date 2015-11-05 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/626150 [access date]
Sub-seafloor metatranscriptomes from anaerobic Peru Margin sediments collected on JOIDES Resolution, Leg 201. Dataset Description: Methods and Sampling: <p><strong>Sample collection and storage: &nbsp;</strong>Subsurface sediment samples from the continental shelf of Peru,&nbsp;Ocean Drilling Program (ODP) Site 1229D (77° 57.4590′ W, 10° 58.5721′ S), were obtained during ODP Leg 201 on 6 March 2002. Careful precautions were taken to avoid contamination during the sampling process. For Integrated Ocean Drilling Program (IODP) cores, contamination tests were performed using perfluorocarbon tracers and fluorescent microspheres. Sediment samples were immediately frozen at −80 degrees&nbsp;C after sampling and stored at −80 degrees C&nbsp;until used for mRNA extractions in this study (10-year storage time at −80 degrees&nbsp;C).</p>
<p><strong>RNA extraction and purification: &nbsp;</strong>Extraction of sub-seafloor RNA was performed according to the protocol described previously.&nbsp;In brief, RNA was extracted from 25 g of sediment using the FastRNA Pro Soil-Direct Kit (MP Biomedicals). It was necessary to scale up the volume of sediment that is typically extracted with the kit (~0.5 g) owing to the low biomass inherent to marine subsurface samples. All tubes, tips and disposables used were certified RNase free and all extraction procedures were performed in a laminar flow hood to reduce aerosol contamination by bacterial and fungal cells/spores. Five 15-ml Lysing Matrix E tubes (MP Biomedicals) were filled with 5 g sediment and 5 ml of Soil Lysis Solution (MP Biomedicals). Tubes were vortexed to suspend the sediment and Soil Lysis Solution was added to the tube leaving 1 ml of headspace.&nbsp;Tubes were then homogenized for 60 s on the FastPrep-24 homogenizer (MP Biomedicals) with a setting of 4.5. Contents were pooled into two 50-ml tubes and centrifuged for 30 min at 4000 r.p.m. (3220g) at room temperature (25 degrees&nbsp;C). Supernatants were combined in a new 50-ml tube and 1/10 volume of 2 M sodium acetate (pH 4.0) was added. An equal volume of phenol-chloroform (pH 6.5) was added and vortexed for 30 s, incubated for 5 min at room temperature, and spun at 4000 r.p.m. (3220g) for 20 min at 4 degrees&nbsp;C. The aqueous phase was transferred to a new 50-ml tube. Nucleic acids were precipitated by adding 2.5 and 1/10 volumes 100% ethanol and 3 M sodium acetate, respectively, and incubating overnight at −80 degrees&nbsp;C. The next day, tubes were spun at 4000 r.p.m. (3220g) for 60 min at 4 degrees&nbsp;C and the supernatant removed. Pellets were washed with 70% ethanol, spun for 15 min at 4 degrees&nbsp;C and air-dried. Dried pellets were resuspended with 0.25 ml RNase-free sterile water and combined into a new 1.5-ml tube. 1/10 volume of 2 M sodium acetate (pH 4.0) and an equal volume of phenol-chloroform (pH 6.5) were added, vortexed for 1 min and incubated for 5 min at room temperature. This was necessary to remove residual organic material (that is, humic acids) resulting from the rather large pellet/precipitate. After centrifuging at 14000 r.p.m. (20817g) for 10 min at 4 degrees&nbsp;C, the top phase was removed into a new 1.5-ml tube. 0.7 volumes of 100% isopropanol was added and incubated for 1 h at −20 degrees&nbsp;C (to precipitate nucleic acids). Tubes were then centrifuged for 20 min at 14000 r.p.m. (20,817g) at 4 degrees&nbsp;C and the supernatant removed. Pellets were washed with 70% ethanol and centrifuged at 14000 r.p.m. (20817g) for 5 min at 4 degrees&nbsp;C. After removing ethanol and air-drying, pellets were re-suspended in 0.2 ml of RNase free sterile water. DNA was removed using the Turbo DNA-free kit (Life Technologies), increasing the incubation time to 1 h to ensure rigorous DNA removal. After this step, samples were taken through the protocol supplied with the FastRNA Pro Soil-Direct kit to the end (starting at the RNA Matrix and RNA Slurry addition step), including the column purification step to remove residual humic acids (see FastRNA Pro Soil-Direct Kit manual). Extraction blanks were performed (adding sterile water instead of sample) to ensure that aerosolized contaminants did not enter sample and reagent tubes during the extraction process. Absence of DNA and RNA contamination was confirmed by no visible amplification of small subunit (SSU) ribosomal RNA (rRNA) and rRNA genes from extraction blanks after 35 cycles of PCR and RT–PCR.</p>
<p>After RNA extraction, the MEGA-Clear RNA Purification Kit (Life Technologies) was used to purify the RNA. This kit removes short RNA fragments (mostly produced during the extraction protocol) and residual inhibitors (that is, humics). We followed the protocol all the way through the optional precipitation/concentration step, re-suspending the RNA pellet in 10 ul of RNase-free sterile water. Before cDNA amplification, the removal of contaminating DNA in RNA extracts was confirmed by the absence of visible amplification of SSU rRNA genes after 35 cycles of PCR using the RNA extracts as template.</p>
<p><strong>cDNA amplification and Illumina sequencing:&nbsp;</strong>Five microlitres of purified RNA was used as template for whole-cDNA amplification using the Ovation RNA-Seq v2 System (NuGEN technologies, <a href="http://www.nugeninc.com/nugen/index.cfm/products/cs/ngs/rna-seq-v2/" target="_blank">http://www.nugeninc.com/nugen/index.cfm/products/cs/ngs/rna-seq-v2/</a>). We followed the manufacturer’s instructions for cDNA amplification, and the resulting quantity of cDNA was checked on a Nanodrop (Thermo Scientific) and Fluorometer (Qubit 2.0, Life Technologies). Quality of the amplified cDNA was checked on a Bioanalyzer (Agilent Biotechnologies) before Illumina sequencing. Illumina library preparation and paired-end sequencing was performed at the University of Delaware Sequencing and Genotyping Center (Delaware Biotechnology Institute).</p>
<p><strong>Related references:</strong><br />
For more sampling information see <a href="http://www-odp.tamu.edu/publications/prelim/201_prel/201toc.html">www-odp.tamu.edu/publications/prelim/201_prel/201toc.html</a><br />
The manuscript is at <a href="http://www.nature.com/nature/journal/v499/n7457/full/nature12230.html" target="_blank">http://www.nature.com/nature/journal/v499/n7457/full/nature12230.html</a></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0939564 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0939564
Funding provided by NSF Division of Integrative Organismal Systems (NSF IOS) Award Number: IOS-1238801 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1238801
completed
William D. Orsi
Woods Hole Oceanographic Institution
+49 89 2180 6598
Richard-Wagner Str. 10
Munich
80333
Germany
w.orsi@lrz.uni-muenchen.de
pointOfContact
Jennifer F. Biddle
University of Delaware
302-645-4267
College of Earth, Ocean, and Environment 212 Cannon Laboratory
Lewes
Delaware
19958
USA
jfbiddle@udel.edu
pointOfContact
Glenn D. Christman
University of Delaware
College of Earth, Ocean, and Environment University of Delaware
Lewes
Delaware
19958
USA
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: 05 November 2015
Unknown
accession_number
SRA_number
description
SRA_URL
accession_URL
Bioanalyzer
Fluorometer
Nanodrop
PCR
theme
None, User defined
accession number
brief description
featureType
BCO-DMO Standard Parameters
Bioanalyzer
Fluorometer
Spectrophotometer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
JRES-201
service
Deployment Activity
Eastern Equatorial Pacific and Peru Margin
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.
Center for Dark Energy Biosphere Investigations
http://www.darkenergybiosphere.org
Center for Dark Energy Biosphere Investigations
The mission of the Center for Dark Energy Biosphere Investigations (C-DEBI) is to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.
C-DEBI provides a framework for a large, multi-disciplinary group of scientists to pursue fundamental questions about life deep in the sub-surface environment of Earth. The fundamental science questions of C-DEBI involve exploration and discovery, uncovering the processes that constrain the sub-surface biosphere below the oceans, and implications to the Earth system. What type of life exists in this deep biosphere, how much, and how is it distributed and dispersed? What are the physical-chemical conditions that promote or limit life? What are the important oxidation-reduction processes and are they unique or important to humankind? How does this biosphere influence global energy and material cycles, particularly the carbon cycle? Finally, can we discern how such life evolved in geological settings beneath the ocean floor, and how this might relate to ideas about the origin of life on our planet?
C-DEBI's scientific goals are pursued with a combination of approaches:
(1) coordinate, integrate, support, and extend the research associated with four major programs—Juan de Fuca Ridge flank (JdF), South Pacific Gyre (SPG), North Pond (NP), and Dorado Outcrop (DO)—and other field sites;
(2) make substantial investments of resources to support field, laboratory, analytical, and modeling studies of the deep subseafloor ecosystems;
(3) facilitate and encourage synthesis and thematic understanding of submarine microbiological processes, through funding of scientific and technical activities, coordination and hosting of meetings and workshops, and support of (mostly junior) researchers and graduate students; and
(4) entrain, educate, inspire, and mentor an interdisciplinary community of researchers and educators, with an emphasis on undergraduate and graduate students and early-career scientists.
Note: Katrina Edwards was a former PI of C-DEBI; James Cowen is a former co-PI.
Data Management:
C-DEBI is committed to ensuring all the data generated are publically available and deposited in a data repository for long-term storage as stated in their Data Management Plan (PDF) and in compliance with the NSF Ocean Sciences Sample and Data Policy. The data types and products resulting from C-DEBI-supported research include a wide variety of geophysical, geological, geochemical, and biological information, in addition to education and outreach materials, technical documents, and samples. All data and information generated by C-DEBI-supported research projects are required to be made publically available either following publication of research results or within two (2) years of data generation.
To ensure preservation and dissemination of the diverse data-types generated, C-DEBI researchers are working with BCO-DMO Data Managers make data publicly available online. The partnership with BCO-DMO helps ensure that the C-DEBI data are discoverable and available for reuse. Some C-DEBI data is better served by specialized repositories (NCBI's GenBank for sequence data, for example) and, in those cases, BCO-DMO provides dataset documentation (metadata) that includes links to those external repositories.
C-DEBI
largerWorkCitation
program
International Ocean Discovery Program
http://www.iodp.org/index.php
International Ocean Discovery Program
The International Ocean Discovery Program (IODP) is an international marine research collaboration that explores Earth's history and dynamics using ocean-going research platforms to recover data recorded in seafloor sediments and rocks and to monitor subseafloor environments. IODP depends on facilities funded by three platform providers with financial contributions from five additional partner agencies. Together, these entities represent 26 nations whose scientists are selected to staff IODP research expeditions conducted throughout the world's oceans.
IODP expeditions are developed from hypothesis-driven science proposals aligned with the program's science plan Illuminating Earth's Past, Present, and Future. The science plan identifies 14 challenge questions in the four areas of climate change, deep life, planetary dynamics, and geohazards.
IODP's three platform providers include:
The U.S. National Science Foundation (NSF)
Japan's Ministry of Education, Culture, Sports, Science and Technology (MEXT)
The European Consortium for Ocean Research Drilling (ECORD)
More information on IODP, including the Science Plan and Policies/Procedures, can be found on their website at http://www.iodp.org/program-documents.
A summary table with links to IODP datasets currently hosted on Zenodo (https://zenodo.org/communities/iodp) can be accessed using the following link: https://iodp.tamu.edu/database/zenodo.html
IODP
largerWorkCitation
program
World-wide exploration of microbial eukaryote diversity and activity in the marine subsurface
https://osprey.bco-dmo.org/project/626119
World-wide exploration of microbial eukaryote diversity and activity in the marine subsurface
<p><em>Project description obtained from <a href="http://www.darkenergybiosphere.org/education/postdocsFunded.html" target="_blank">C-DEBI</a>:</em><br />
Practically nothing is known about microbial eukaryotes (mEuks) in the marine subsurface. mEuks are pivotal members of microbial communities because they regenerate nutrients and modify or remineralize organic matter through grazing on prokaryotic and other eukaryotic prey. Thus, mEuks help determine metabolic potentials of microbial communities and influence elemental cycling. Only one study has addressed mEuk diversity in the marine subsurface (Edgcomb et al. 2010), which suggested Fungi dominate the eukaryotic subsurface community and are active in sediments 35 mbsf at the Peru Margin. Thus, some mEuks may be specifically adapted to the deep subsurface and may play significant roles in the utilization and regeneration of organic matter and nutrients in deep-sea sediments. </p>
<p>One objective of this study will be to further investigate whether Fungi are consistently the dominant group of mEuks in the marine subsurface by examining mEuk diversity in a broad range of subsurface samples from ODP expeditions spanning the world’s oceans. Deep sequencing of SSU rRNA in these samples will provide a proxy for mEuk diversity and activity in the marine subsurface. A second objective will be to ‘ground truth’ an mRNA isolation protocol for mEuks in marine subsurface sediments. Once established, this protocol will enable the third objective, which is the creation of a eukaryotic metatranscriptome from ODP site 1229. This metatranscriptome will provide insights into the functional role of mEuks in the marine subsurface and perhaps new insights into microbial evolution.</p>
<p>This project was funded by a C-DEBI Postdoctoral Fellowship.</p>
Microbial Euk Div Mar Subsurface
largerWorkCitation
project
eng; USA
biota
oceans
Eastern Equatorial Pacific and Peru Margin
2015-11-05
Peru Margin
0
BCO-DMO catalogue of parameters from Sub-seafloor metatranscriptomes from anaerobic Peru Margin sediments collected on R/V JOIDES Resolution Leg 201 in 2002
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/626168.rdf
Name: accession_number
Units: dimensionless
Description: <p>NCBI accession number.<br />
</p>
http://lod.bco-dmo.org/id/dataset-parameter/626169.rdf
Name: SRA_number
Units: dimensionless
Description: <p>NCBI SRA accession number.<br />
</p>
http://lod.bco-dmo.org/id/dataset-parameter/626170.rdf
Name: description
Units: dimensionless
Description: <p>Brief description of the sequence.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626171.rdf
Name: SRA_URL
Units: dimensionless
Description: <p>Hyperlink to NCBI SRA accession.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626172.rdf
Name: accession_URL
Units: dimensionless
Description: <p>Hyperlink to NCBI accession.</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
1554
https://datadocs.bco-dmo.org/file/g77yqvMtwgEw1Y/peru_margin.csv
peru_margin.csv
Primary data file for dataset ID 626150
download
https://osprey.bco-dmo.org/dataset/626150/data/download
download
onLine
dataset
<p><strong>Sample collection and storage: &nbsp;</strong>Subsurface sediment samples from the continental shelf of Peru,&nbsp;Ocean Drilling Program (ODP) Site 1229D (77° 57.4590′ W, 10° 58.5721′ S), were obtained during ODP Leg 201 on 6 March 2002. Careful precautions were taken to avoid contamination during the sampling process. For Integrated Ocean Drilling Program (IODP) cores, contamination tests were performed using perfluorocarbon tracers and fluorescent microspheres. Sediment samples were immediately frozen at −80 degrees&nbsp;C after sampling and stored at −80 degrees C&nbsp;until used for mRNA extractions in this study (10-year storage time at −80 degrees&nbsp;C).</p>
<p><strong>RNA extraction and purification: &nbsp;</strong>Extraction of sub-seafloor RNA was performed according to the protocol described previously.&nbsp;In brief, RNA was extracted from 25 g of sediment using the FastRNA Pro Soil-Direct Kit (MP Biomedicals). It was necessary to scale up the volume of sediment that is typically extracted with the kit (~0.5 g) owing to the low biomass inherent to marine subsurface samples. All tubes, tips and disposables used were certified RNase free and all extraction procedures were performed in a laminar flow hood to reduce aerosol contamination by bacterial and fungal cells/spores. Five 15-ml Lysing Matrix E tubes (MP Biomedicals) were filled with 5 g sediment and 5 ml of Soil Lysis Solution (MP Biomedicals). Tubes were vortexed to suspend the sediment and Soil Lysis Solution was added to the tube leaving 1 ml of headspace.&nbsp;Tubes were then homogenized for 60 s on the FastPrep-24 homogenizer (MP Biomedicals) with a setting of 4.5. Contents were pooled into two 50-ml tubes and centrifuged for 30 min at 4000 r.p.m. (3220g) at room temperature (25 degrees&nbsp;C). Supernatants were combined in a new 50-ml tube and 1/10 volume of 2 M sodium acetate (pH 4.0) was added. An equal volume of phenol-chloroform (pH 6.5) was added and vortexed for 30 s, incubated for 5 min at room temperature, and spun at 4000 r.p.m. (3220g) for 20 min at 4 degrees&nbsp;C. The aqueous phase was transferred to a new 50-ml tube. Nucleic acids were precipitated by adding 2.5 and 1/10 volumes 100% ethanol and 3 M sodium acetate, respectively, and incubating overnight at −80 degrees&nbsp;C. The next day, tubes were spun at 4000 r.p.m. (3220g) for 60 min at 4 degrees&nbsp;C and the supernatant removed. Pellets were washed with 70% ethanol, spun for 15 min at 4 degrees&nbsp;C and air-dried. Dried pellets were resuspended with 0.25 ml RNase-free sterile water and combined into a new 1.5-ml tube. 1/10 volume of 2 M sodium acetate (pH 4.0) and an equal volume of phenol-chloroform (pH 6.5) were added, vortexed for 1 min and incubated for 5 min at room temperature. This was necessary to remove residual organic material (that is, humic acids) resulting from the rather large pellet/precipitate. After centrifuging at 14000 r.p.m. (20817g) for 10 min at 4 degrees&nbsp;C, the top phase was removed into a new 1.5-ml tube. 0.7 volumes of 100% isopropanol was added and incubated for 1 h at −20 degrees&nbsp;C (to precipitate nucleic acids). Tubes were then centrifuged for 20 min at 14000 r.p.m. (20,817g) at 4 degrees&nbsp;C and the supernatant removed. Pellets were washed with 70% ethanol and centrifuged at 14000 r.p.m. (20817g) for 5 min at 4 degrees&nbsp;C. After removing ethanol and air-drying, pellets were re-suspended in 0.2 ml of RNase free sterile water. DNA was removed using the Turbo DNA-free kit (Life Technologies), increasing the incubation time to 1 h to ensure rigorous DNA removal. After this step, samples were taken through the protocol supplied with the FastRNA Pro Soil-Direct kit to the end (starting at the RNA Matrix and RNA Slurry addition step), including the column purification step to remove residual humic acids (see FastRNA Pro Soil-Direct Kit manual). Extraction blanks were performed (adding sterile water instead of sample) to ensure that aerosolized contaminants did not enter sample and reagent tubes during the extraction process. Absence of DNA and RNA contamination was confirmed by no visible amplification of small subunit (SSU) ribosomal RNA (rRNA) and rRNA genes from extraction blanks after 35 cycles of PCR and RT–PCR.</p>
<p>After RNA extraction, the MEGA-Clear RNA Purification Kit (Life Technologies) was used to purify the RNA. This kit removes short RNA fragments (mostly produced during the extraction protocol) and residual inhibitors (that is, humics). We followed the protocol all the way through the optional precipitation/concentration step, re-suspending the RNA pellet in 10 ul of RNase-free sterile water. Before cDNA amplification, the removal of contaminating DNA in RNA extracts was confirmed by the absence of visible amplification of SSU rRNA genes after 35 cycles of PCR using the RNA extracts as template.</p>
<p><strong>cDNA amplification and Illumina sequencing:&nbsp;</strong>Five microlitres of purified RNA was used as template for whole-cDNA amplification using the Ovation RNA-Seq v2 System (NuGEN technologies, <a href="http://www.nugeninc.com/nugen/index.cfm/products/cs/ngs/rna-seq-v2/" target="_blank">http://www.nugeninc.com/nugen/index.cfm/products/cs/ngs/rna-seq-v2/</a>). We followed the manufacturer’s instructions for cDNA amplification, and the resulting quantity of cDNA was checked on a Nanodrop (Thermo Scientific) and Fluorometer (Qubit 2.0, Life Technologies). Quality of the amplified cDNA was checked on a Bioanalyzer (Agilent Biotechnologies) before Illumina sequencing. Illumina library preparation and paired-end sequencing was performed at the University of Delaware Sequencing and Genotyping Center (Delaware Biotechnology Institute).</p>
<p><strong>Related references:</strong><br />
For more sampling information see <a href="http://www-odp.tamu.edu/publications/prelim/201_prel/201toc.html">www-odp.tamu.edu/publications/prelim/201_prel/201toc.html</a><br />
The manuscript is at <a href="http://www.nature.com/nature/journal/v499/n7457/full/nature12230.html" target="_blank">http://www.nature.com/nature/journal/v499/n7457/full/nature12230.html</a></p>
Specified by the Principal Investigator(s)
<p>Quality control of the data set was performed using FastQC (<a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" target="_blank">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/</a>), with a quality score cutoff of 28. Approximately 1 billion paired-end reads that passed quality control were imported into CLC Genomics Workbench 5.0 (CLC Bio) and assembled using the paired-end Illumina assembler. Contigs were assembled over a range of k-mer sizes (20, 50, 60, 64) with a minimum contig size cutoff of 300 nucleotides. The k-mer size of 50 resulted in the highest number of contigs and these contigs were chosen for use in downstream analyses. To reduce the formation of chimaeric assemblies, we used a paired-end sequencing approach and performed assemblies without scaffolding. Reads were mapped onto the contigs using the read mapping option in CLC Genomics Workbench to retain information on relative abundance of contigs.&nbsp;Quality-filtered reads and raw reads are publicly available through the NCBI SRA at <a href="http://www.ncbi.nlm.nih.gov/sra?term=SRA058813" target="_blank">http://www.ncbi.nlm.nih.gov/sra?term=SRA058813</a></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
Bioanalyzer
Bioanalyzer
PI Supplied Instrument Name: Bioanalyzer PI Supplied Instrument Description:Quality of the amplified cDNA was checked on a Bioanalyzer (Agilent Biotechnologies) before Illumina sequencing. Instrument Name: Bioanalyzer Instrument Short Name:Bioanalyzer Instrument 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.
Fluorometer
Fluorometer
PI Supplied Instrument Name: Fluorometer PI Supplied Instrument Description:We followed the manufacturer’s instructions for cDNA amplification, and the resulting quantity of cDNA was checked on a Nanodrop (Thermo Scientific) and Fluorometer (Qubit 2.0, Life Technologies). Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
Nanodrop
Nanodrop
PI Supplied Instrument Name: Nanodrop PI Supplied Instrument Description:We followed the manufacturer’s instructions for cDNA amplification, and the resulting quantity of cDNA was checked on a Nanodrop (Thermo Scientific) and Fluorometer (Qubit 2.0, Life Technologies). Instrument Name: Spectrophotometer Instrument Short Name:Spectrophotometer Instrument Description: An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/
PCR
PCR
PI Supplied Instrument Name: PCR PI Supplied Instrument Description:Absence of DNA and RNA contamination was confirmed by no visible amplification of small subunit (SSU) ribosomal RNA (rRNA) and rRNA genes from extraction blanks after 35 cycles of PCR and RT–PCR. Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument 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)
Cruise: JRES-201
JRES-201
R/V JOIDES Resolution
Community Standard Description
International Council for the Exploration of the Sea
R/V JOIDES Resolution
vessel
JRES-201
Steven L. D'Hondt
University of Rhode Island
http://dmoserv3.whoi.edu/data_docs/C-DEBI/cruise_reports/201PREL-1.pdf
Report describing JRES-201
R/V JOIDES Resolution
Community Standard Description
International Council for the Exploration of the Sea
R/V JOIDES Resolution
vessel