http://lod.bco-dmo.org/id/dataset/745527
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
2018-09-04
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
NCBI accession metadata for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 2014
2018-09-04
publication
2018-09-04
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-07-24
publication
https://doi.org/10.1575/1912/bco-dmo.745527.1
David Caron
University of Southern California
principalInvestigator
Sarah K. Hu
University of Southern California
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: Caron, D., Hu, S. (2018) NCBI accession metadata for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 2014. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-09-04 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.745527.1 [access date]
Dataset Description: <p>These data were published in Hu et al., 2016.<br />
Sequence data can be found in the NCBI SRA database under accession number&nbsp;<a href="https://www.ncbi.nlm.nih.gov/sra/SRP070577" target="_blank">SRP070577</a>&nbsp;with the associated&nbsp;BioProject&nbsp;<a href="https://www.ncbi.nlm.nih.gov//bioproject/PRJNA311248" target="_blank">PRJNA311248</a>.</p> Methods and Sampling: <p>Samples were collected seasonally at the San Pedro Ocean Time-series (SPOT) station at four depths (surface, subsurface chlorophyll maximum, 150 and 890 m).&nbsp;The SPOT station was sampled from 5 m, the subsurface chlorophyll maximum (SCM), 150 and 890 m using 10 L Niskin bottles mounted on a CTD rosette, during regularly scheduled cruises (https://dornsife.usc.edu/spot/).</p>
<p>Seawater from all samples was sequentially pre-filtered through 200 μm and 80 μm Nitex mesh to reduce abundances of multicellular eukaryotes (metazoa). Near-surface and SCM seawater (2 L) and 150 and 890 m seawater (4 L) was filtered onto GF/F filters (nominal pore size 0.7 μm; Whatman, International Ltd, Florham Park, NJ, USA) and immediately flash frozen in liquid nitrogen for later DNA and RNA extraction.</p>
<p>Total DNA and RNA were extracted simultaneously from each sample using the All Prep DNA/RNA Mini kit (Qiagen, Valencia, CA, USA, #80204). Genomic DNA was removed during the RNA extraction with RNase-Free DNase reagents (Qiagen, #79254). Total extracted RNA was checked for residual genomic DNA by performing a polymerase chain reaction (PCR) using DNA specific primers to ensure that no amplified products appeared when run on an agarose gel. RNA was reverse transcribed into cDNA using iScript Reverse Transcription Supermix with random hexamers (Bio-Rad Laboratories, Hercules, CA, USA, #170-8840).</p>
<p>The resulting cDNA and DNA from each sample were PCR amplified using V4 forward (5′&nbsp;-CCAGCA[GC]C[CT]GCGGTA ATTCC-3′&nbsp;) and reverse (5′&nbsp;-ACTTTCGTTCTTGAT[CT][AG]A-3′&nbsp;) primers (Stoeck <em>et al</em>. 2010). Duplicate PCR reactions were performed in 50 μL volumes of: 1X Phusion High-Fidelity DNA buffer, 1 unit of Phusion DNA polymerase (New England Biolabs, Ipswich, MA, USA, #M0530S), 200 μM of dNTPs, 0.5 μM of each V4 forward and reverse primer, 3% DMSO, 50 mM of MgCl and 5 ng of either DNA or cDNA template per reaction. The PCR thermal cycler program consisted of a 98◦C denaturation step for 30 s, followed by 10 cycles of 10 s at 98◦C, 30 s at 53◦C and 30 s at 72◦C, and then 15 cycles of 10 s at 98◦C, 30 s at 48◦C and 30 s at 72◦C, and a final elongation step at 72◦C for 10 min, as described in Rodrı ́guez-Martı ́nez <em>et al</em>. (2012). PCR products were purified (Qiagen, #28104) and duplicate samples were pooled. The ∼400 bp cDNA and DNA PCR products were quality checked on an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).</p>
<p>Sampling Locations:<br />
SPOT (33◦ 33′ N, 118◦ 24′ W) - surface, DCM, 150 m, and 890 m<br />
Port of LA (33◦ 42.75′ N, 118◦ 15.55′ W) - surface<br />
Catalina (33◦ 27.17′ N, 118◦ 28.51′ W)-surface</p>
<p>For protocols see:<br />
<a href="https://www.protocols.io/view/sample-collection-from-the-field-for-downstream-mo-hisb4ee" target="_blank">https://www.protocols.io/view/sample-collection-from-the-field-for-downstream-mo-hisb4ee</a><br />
<a href="https://www.protocols.io/view/rna-and-optional-dna-extraction-from-environmental-hk3b4yn" target="_blank">https://www.protocols.io/view/rna-and-optional-dna-extraction-from-environmental-hk3b4yn</a><br />
<a href="https://www.protocols.io/view/18s-v4-tag-sequencing-pcr-amplification-and-librar-hdmb246" target="_blank">https://www.protocols.io/view/18s-v4-tag-sequencing-pcr-amplification-and-librar-hdmb246</a></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1737409 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1737409
completed
David Caron
University of Southern California
213-740-0203
Dornsife College of Letters, Arts, and Sciences 3616 Trousdale Parkway
Los Angeles
CA
90089
USA
dcaron@usc.edu
pointOfContact
Sarah K. Hu
University of Southern California
skhu@tamu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
bioproject_accession
sample_name
SRA_run_ID
SRA_run_link
library_ID
SRA_study_ID
SRA_title
library_strategy
library_source
library_selection
library_layout
platform
instrument_model
design_description
filetype
filename
filetpe2
filename2
Depth
lat
lon
Illumina MiSeq
theme
None, User defined
No BCO-DMO term
platform
latitude
longitude
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
CTD Sea-Bird SBE 911plus
Niskin bottle
instrument
BCO-DMO Standard Instruments
SPOT_Yellowfin_Cruises
service
Deployment Activity
San Pedro Ocean Time Series
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.
Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series
https://osprey.bco-dmo.org/project/743049
Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series
<p>Planktonic marine microbial communities consist of a diverse collection of bacteria, archaea, viruses, protists (phytoplankton and protozoa) and small animals (metazoan). Collectively, these species are responsible for virtually all marine pelagic primary production where they form the basis of food webs and carry out a large fraction of respiratory processes. Microbial interactions include the traditional role of predation, but recent research recognizes the importance of parasitism, symbiosis and viral infection. Characterizing the response of pelagic microbial communities and processes to environmental influences is fundamental to understanding and modeling carbon flow and energy utilization in the ocean, but very few studies have attempted to study all of these assemblages in the same study. This project is comprised of long-term (monthly) and short-term (daily) sampling at the San Pedro Ocean Time-series (SPOT) site. Analysis of the resulting datasets investigates co-occurrence patterns of microbial taxa (e.g. protist-virus and protist-prokaryote interactions, both positive and negative) indicating which species consistently co-occur and potentially interact, followed by examination gene expression to help define the underlying mechanisms. This study augments 20 years of baseline studies of microbial abundance, diversity, rates at the site, and will enable detection of low-frequency changes in composition and potential ecological interactions among microbes, and their responses to changing environmental forcing factors. These responses have important consequences for higher trophic levels and ocean-atmosphere feedbacks. The broader impacts of this project include training graduate and undergraduate students, providing local high school student with summer lab experiences, and PI presentations at local K-12 schools, museums, aquaria and informal learning centers in the region. Additionally, the PIs advise at the local, county and state level regarding coastal marine water quality.</p>
<p>This research project is unique in that it is a holistic study (including all microbes from viruses to small metazoa) of microbial species diversity and ecological activities, carried out at the SPOT site off the coast of southern California. In studying all microbes simultaneously, this work aims to identify important ecological interactions among microbial species, and identify the basis(es) for those interactions. This research involves (1) extensive analyses of prokaryote (archaean and bacterial) and eukaryote (protistan and micro-metazoan) diversity via the sequencing of marker genes, (2) studies of whole-community gene expression by eukaryotes and prokaryotes in order to identify key functional characteristics of microorganismal groups and the detection of active viral infections, and (3) metagenomic analysis of viruses and bacteria to aid interpretation of transcriptomic analyses using genome-encoded information. The project includes exploratory metatranscriptomic analysis of poorly-understood aphotic and hypoxic-zone protists, to examine their stratification, functions and hypothesized prokaryotic symbioses.</p>
SPOT
largerWorkCitation
project
eng; USA
oceans
San Pedro Ocean Time Series
-118.475167
-118.259167
33.452833
33.7125
2013-04-24
2014-01-15
San Pedro Channel off the coast of Los Angeles
0
BCO-DMO catalogue of parameters from NCBI accession metadata for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 2014
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/745569.rdf
Name: bioproject_accession
Units: unitless
Description: <p>NCBI BioProject identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/745570.rdf
Name: sample_name
Units: unitless
Description: <p>Sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/745571.rdf
Name: SRA_run_ID
Units: unitless
Description: <p>SRA Run identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/745572.rdf
Name: SRA_run_link
Units: unitless
Description: <p>URL for SRA Run Page at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/745573.rdf
Name: library_ID
Units: unitless
Description: <p>SRA title</p>
http://lod.bco-dmo.org/id/dataset-parameter/745574.rdf
Name: SRA_study_ID
Units: unitless
Description: <p>SRA study identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/745575.rdf
Name: SRA_title
Units: unitless
Description: <p>Descriptive title of SRA accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/745576.rdf
Name: library_strategy
Units: unitless
Description: <p>Library strategy ("AMPLICON")</p>
http://lod.bco-dmo.org/id/dataset-parameter/745577.rdf
Name: library_source
Units: unitless
Description: <p>Library source ("TRANSCRIPTOMIC" or "GENOMIC")</p>
http://lod.bco-dmo.org/id/dataset-parameter/745578.rdf
Name: library_selection
Units: unitless
Description: <p>Library selection ("PCR")</p>
http://lod.bco-dmo.org/id/dataset-parameter/745579.rdf
Name: library_layout
Units: unitless
Description: <p>Library layout ("paired")</p>
http://lod.bco-dmo.org/id/dataset-parameter/745580.rdf
Name: platform
Units: unitless
Description: <p>Sequencing platform ("Illumina")</p>
http://lod.bco-dmo.org/id/dataset-parameter/745581.rdf
Name: instrument_model
Units: unitless
Description: <p>Sequencing instrument model ("Illumina MiSeq")</p>
http://lod.bco-dmo.org/id/dataset-parameter/745582.rdf
Name: design_description
Units: unitless
Description: <p>Sequencing design description</p>
http://lod.bco-dmo.org/id/dataset-parameter/745583.rdf
Name: filetype
Units: unitless
Description: <p>Type of file 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/745584.rdf
Name: filename
Units: unitless
Description: <p>Name of file 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/745585.rdf
Name: filetpe2
Units: unitless
Description: <p>Type of file 2</p>
http://lod.bco-dmo.org/id/dataset-parameter/745586.rdf
Name: filename2
Units: unitless
Description: <p>Name of file 2</p>
http://lod.bco-dmo.org/id/dataset-parameter/745587.rdf
Name: Depth
Units: various
Description: <p>Nominal depth ("Surface" or number of meters) of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/745588.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/745589.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude of sample collection</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
28488
https://darchive.mblwhoilibrary.org/bitstream/1912/24365/1/dataset-745527_18s-rrna-gene-tag-sequences-dna-and-rna__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.745527.1
download
onLine
dataset
<p>Samples were collected seasonally at the San Pedro Ocean Time-series (SPOT) station at four depths (surface, subsurface chlorophyll maximum, 150 and 890 m).&nbsp;The SPOT station was sampled from 5 m, the subsurface chlorophyll maximum (SCM), 150 and 890 m using 10 L Niskin bottles mounted on a CTD rosette, during regularly scheduled cruises (https://dornsife.usc.edu/spot/).</p>
<p>Seawater from all samples was sequentially pre-filtered through 200 μm and 80 μm Nitex mesh to reduce abundances of multicellular eukaryotes (metazoa). Near-surface and SCM seawater (2 L) and 150 and 890 m seawater (4 L) was filtered onto GF/F filters (nominal pore size 0.7 μm; Whatman, International Ltd, Florham Park, NJ, USA) and immediately flash frozen in liquid nitrogen for later DNA and RNA extraction.</p>
<p>Total DNA and RNA were extracted simultaneously from each sample using the All Prep DNA/RNA Mini kit (Qiagen, Valencia, CA, USA, #80204). Genomic DNA was removed during the RNA extraction with RNase-Free DNase reagents (Qiagen, #79254). Total extracted RNA was checked for residual genomic DNA by performing a polymerase chain reaction (PCR) using DNA specific primers to ensure that no amplified products appeared when run on an agarose gel. RNA was reverse transcribed into cDNA using iScript Reverse Transcription Supermix with random hexamers (Bio-Rad Laboratories, Hercules, CA, USA, #170-8840).</p>
<p>The resulting cDNA and DNA from each sample were PCR amplified using V4 forward (5′&nbsp;-CCAGCA[GC]C[CT]GCGGTA ATTCC-3′&nbsp;) and reverse (5′&nbsp;-ACTTTCGTTCTTGAT[CT][AG]A-3′&nbsp;) primers (Stoeck <em>et al</em>. 2010). Duplicate PCR reactions were performed in 50 μL volumes of: 1X Phusion High-Fidelity DNA buffer, 1 unit of Phusion DNA polymerase (New England Biolabs, Ipswich, MA, USA, #M0530S), 200 μM of dNTPs, 0.5 μM of each V4 forward and reverse primer, 3% DMSO, 50 mM of MgCl and 5 ng of either DNA or cDNA template per reaction. The PCR thermal cycler program consisted of a 98◦C denaturation step for 30 s, followed by 10 cycles of 10 s at 98◦C, 30 s at 53◦C and 30 s at 72◦C, and then 15 cycles of 10 s at 98◦C, 30 s at 48◦C and 30 s at 72◦C, and a final elongation step at 72◦C for 10 min, as described in Rodrı ́guez-Martı ́nez <em>et al</em>. (2012). PCR products were purified (Qiagen, #28104) and duplicate samples were pooled. The ∼400 bp cDNA and DNA PCR products were quality checked on an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).</p>
<p>Sampling Locations:<br />
SPOT (33◦ 33′ N, 118◦ 24′ W) - surface, DCM, 150 m, and 890 m<br />
Port of LA (33◦ 42.75′ N, 118◦ 15.55′ W) - surface<br />
Catalina (33◦ 27.17′ N, 118◦ 28.51′ W)-surface</p>
<p>For protocols see:<br />
<a href="https://www.protocols.io/view/sample-collection-from-the-field-for-downstream-mo-hisb4ee" target="_blank">https://www.protocols.io/view/sample-collection-from-the-field-for-downstream-mo-hisb4ee</a><br />
<a href="https://www.protocols.io/view/rna-and-optional-dna-extraction-from-environmental-hk3b4yn" target="_blank">https://www.protocols.io/view/rna-and-optional-dna-extraction-from-environmental-hk3b4yn</a><br />
<a href="https://www.protocols.io/view/18s-v4-tag-sequencing-pcr-amplification-and-librar-hdmb246" target="_blank">https://www.protocols.io/view/18s-v4-tag-sequencing-pcr-amplification-and-librar-hdmb246</a></p>
Specified by the Principal Investigator(s)
<p>Nucleotide bases with a Q score lower than 20 for the last 30 bp of each sequence were trimmed. Paired-end sequences were merged using FLASh (Magoc and Salzberg 2011) with a minimum of 10 bp and maximum of 150 bp overlap between each sequence pair. Sequences shorter than 350 bp, longer than 460 bp, or which had an average quality score lower than 25 were discarded using QIIME v1.8 (Caporaso <em>et al</em>. 2010). Chimeric sequences were identified and removed, by either <em>de novo </em>or reference-based chimera checking (identify chimeric seqs.py in QIIME, intersection method).&nbsp;</p>
<p>The code release v2 associated with this version of the dataset can be downloaded as a .zip file from the Supplemental&nbsp;Documents section of this page. Future code updates will be accessible from the GitHub repository&nbsp;<a href="https://github.com/shu251/V4_tagsequencing_18Sdiversity_q1">https://github.com/shu251/V4_tagsequencing_18Sdiversity_q1</a>.</p>
<p><strong>BCO-DMO Data Manager Processing Notes:</strong><br />
* File "SRA_metadata_finalSHU.xlsx" imported into the BCO-DMO data system.<br />
* Added SRA_run_ids from file "Listof_SRA_IDs.xlsx."<br />
* added a conventional header with dataset name, PI name, version date<br />
* modified parameter names to conform with BCO-DMO naming conventions<br />
* blank values in this dataset are displayed as "nd" for "no data."&nbsp; nd is the default missing data identifier in the BCO-DMO system.<br />
* Split lat_lon column into "lat" and "lon" in decimal degrees.<br />
* Added active html links to dataset for SRA Run IDs<br />
*&nbsp; For curatorial purposes and to satisfy the OCE Sample and Data Policy requirements, the contributor's github was forked to BCO-DMO's github, a release was made, and the .zip file containing that release downloaded to BCO-DMO's data servers.&nbsp;<br />
&nbsp; &nbsp;* BCODMO/V4_tagsequencing_18Sdiversity_q1 forked from shu251/V4_tagsequencing_18Sdiversity_q1<br />
&nbsp; &nbsp;* Release v2 created:&nbsp;https://github.com/BCODMO/V4_tagsequencing_18Sdiversity_q1/tree/v2</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 MiSeq
Illumina MiSeq
PI Supplied Instrument Name: Illumina MiSeq 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: Instrument Name: CTD Sea-Bird SBE 911plus Instrument Short Name:CTD SBE 911plus Instrument Description: The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0058/
PI Supplied Instrument Name: 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: SPOT_Yellowfin_Cruises
SPOT_Yellowfin_Cruises
R/V Yellowfin
R/V Yellowfin
vessel
R/V Yellowfin
R/V Yellowfin
vessel