http://lod.bco-dmo.org/id/dataset/661835
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
2016-10-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Taxonomic binning of transcripts from samples collected during the SIMCO1 (July 2014) and SIMCO2 (Oct 2014) incubation experiments on the linkage between DOM changes and microbial transcription patterns at Sapelo Island, GA.
2016-10-26
publication
2016-10-26
revision
BCO-DMO Linked Data URI
2016-10-26
creation
http://lod.bco-dmo.org/id/dataset/661835
Mary Ann Moran
University of Georgia
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: Moran, M. (2016) Taxonomic binning of transcripts from samples collected during the SIMCO1 (July 2014) and SIMCO2 (Oct 2014) incubation experiments on the linkage between DOM changes and microbial transcription patterns at Sapelo Island, GA. Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2016-10-26 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/661835 [access date]
Taxonomic binning of transcripts from samples collected during the SIMCO1 and SIMCO2 Dataset Description: <p>Incubation experiments examining concurrent changes in DOC composition and microbial transcription patterns were carried out in July 2014 (SIMCO1) and October 2014 (SIMCO2) at Sapelo Island, GA. This dataset contains the taxonomic assignments of transcripts to reference genome bins. Cells were collected by filtration at the time of initial surface water collection (Time 0) and after a 24 hr incubation (Time 24) for both high and low tide water collections on each of the two sample dates. Filters were processed for RNA extraction and mRNA-enriched material was sequenced on an Illumina HiSeq2500 run to produce single-end 250 bp reads.</p> Methods and Sampling: <p>Water samples were collected from Marsh Landing Dock on Sapelo Island GA, prefiltered through a 3 micron membrane filter to remove most eukaryotic microbes, and incubated in 10 L carboys in situ in the dark for 24 h. At the beginning and end of the incubation, three carboys were sacrificed for nucleic acid extraction on 0.2 micron membrane filters, and microbial transcripts were analyzed from two of the three replicates according to methods in Satinsky et al. 2013 and 2014 and protocols.io (https://www.protocols.io/g/moran-lab).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1356010 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1356010
completed
Mary Ann Moran
University of Georgia
706-542-6481
Department of Marine Sciences
Athens
GA
30602
USA
mmoran@uga.edu
pointOfContact
asNeeded
Unknown
sample
organism_strain
transcripts_per_L
Illumina HiSeq2500
theme
None, User defined
sample identification
sample description
count
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
Moran_Sapelo_2012-14
service
Deployment Activity
Sapelo Island, GA
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.
High Resolution Linkages Between DOC Turnover and Bacterioplankton in a Coastal Ocean
https://osprey.bco-dmo.org/project/472758
High Resolution Linkages Between DOC Turnover and Bacterioplankton in a Coastal Ocean
<p><em>Description from NSF award abstract:</em><br />
Long-standing questions regarding the fate of dissolved organic carbon (DOC) in coastal oceans require a better understanding of the network that links bacterioplankton metabolism with carbon transformation. These questions address uncertainties about the composition of the bioreactive DOC components transformed in ocean margins, and the role of bacterial taxonomic and genetic composition in determining the fate of DOC.</p>
<p>This project will infuse a new type of data into coastal carbon cycle research based on high-resolution chemical analysis coupled with bacterial gene expression measures. It will extend DOC process studies down to the single-compound level and bacterial activity studies down to the single-gene level, and integrate this information into existing bioinformatic resources for biogeochemical and modeling applications.</p>
<p>The specific goals of this project are:<br />
1) To reconstruct major components of the network linking DOC composition, DOC turnover, and bacterial heterotrophy in the coastal ocean (the composition of the DOC pool, the major bioreactive components, the bacterioplankton taxa mediating transformations, and the bacterial genes and pathways responsible).</p>
<p>2) To test hypothesized network links for selected DOC compounds using a simplified system that queries individual DOC compounds against a complex natural microbial community.</p>
<p>3) To test hypothesized network links for marine bacteria using a simplified system that queries a single generalist heterotrophic bacteria against a complex natural DOC pool.</p>
<p>4) To verify predicted DOC-gene linkages that are most informative about heterotrophic activities of bacterioplankton.</p>
<p>This research addresses fundamental questions on bacterial mediation of organic carbon fate in the ocean and atmosphere. As such, these investigations linking the chemical changes in dissolved organic carbon with patterns of gene expression in coastal bacterioplankton communities will be of interest to scientists across several disciplines.</p>
<p>---------------------------</p>
<p>Note: The project acronym, SIMCO, means "Sapelo Island Microbial Carbon Observatory".</p>
SIMCO
largerWorkCitation
project
eng; USA
biota
oceans
Sapelo Island, GA
2016-10-26
Southeastern U.S. coastal ocean, 31.4° N Lat, 81.3° W Lon
0
BCO-DMO catalogue of parameters from Taxonomic binning of transcripts from samples collected during the SIMCO1 (July 2014) and SIMCO2 (Oct 2014) incubation experiments on the linkage between DOM changes and microbial transcription patterns at Sapelo Island, GA.
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/661858.rdf
Name: sample
Units: unitless
Description: <p>sample identification: S1 or S2 = SIMCO experiment 1 or 2; L = low tide; H = high tide; 0 = 0 hour incubation; 24 = 24 hour incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/661859.rdf
Name: organism_strain
Units: unitless
Description: <p>description of organism and strain</p>
http://lod.bco-dmo.org/id/dataset-parameter/661860.rdf
Name: transcripts_per_L
Units: transcripts/liter
Description: <p>number of transcripts per liter</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
517989
https://datadocs.bco-dmo.org/file/6YYMloqUov32Bq/taxonomy_all.csv
taxonomy_all.csv
Primary data file for dataset ID 661835
download
https://osprey.bco-dmo.org/dataset/661835/data/download
download
onLine
dataset
<p>Water samples were collected from Marsh Landing Dock on Sapelo Island GA, prefiltered through a 3 micron membrane filter to remove most eukaryotic microbes, and incubated in 10 L carboys in situ in the dark for 24 h. At the beginning and end of the incubation, three carboys were sacrificed for nucleic acid extraction on 0.2 micron membrane filters, and microbial transcripts were analyzed from two of the three replicates according to methods in Satinsky et al. 2013 and 2014 and protocols.io (https://www.protocols.io/g/moran-lab).</p>
Specified by the Principal Investigator(s)
<p>Reads were put through a quality control pipeline that removed rRNAs and internal standards added for quantification (Satinsky et al. 2013). Putative protein encoding reads were analyzed by RAPSearch2 (http://omics.informatics.indiana.edu/mg/RAPSearch2/) against a custom reference database of genomes and transcriptomes compiled from marine bacteria, archaea, and microbial eukaryotes; the database is available for download at: http://ssharma.marsci.uga.edu/Lab/MarineRef2/.</p>
<p><strong>References:</strong><br />
Brandon M. Satinsky, Scott M. Gifford, Byron C. Crump, Mary Ann Moran, 2013. Chapter 12: "Use of Internal Standards for Quantitative Metatranscriptome and Metagenome Analysis" in&nbsp;Methods in Enzymology, Vol. 531.&nbsp;ISSN 0076-6879,&nbsp;http://dx.doi.org/10.1016/B978-0-12-407863-5.00012-5.</p>
<p>Brandon M. Satinskya, Byron C. Crumpb, Christa B. Smithc, Shalabh Sharmac, Brian L. Zielinskid, Mary Dohertye, Jun Mengc, Shulei Sunf, Patricia M. Medeirosc, John H. Pauld, Victoria J. Colese, Patricia L. Yagerc, and Mary Ann Moranc. 2014. Microspatial gene expression patterns in the Amazon River Plume. PNAS 111(30):11085-11090. www.pnas.org/cgi/doi/10.1073/pnas.1402782111</p>
<p><strong>BCO-DMO Processing:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- column names reformatted to comply with BCO-DMO standards<br />
- replaced spaces with underscores<br />
- replaced commas with semi-colons<br />
- replaced str. and Strain with strain</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 HiSeq2500
Illumina HiSeq2500
PI Supplied Instrument Name: Illumina HiSeq2500 PI Supplied Instrument Description:mRNA-enriched material was sequenced 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.
Deployment: Moran_Sapelo_2012-14
Moran_Sapelo_2012-14
Univ_Georgia
laboratory
Moran_Sapelo_2012-14
Mary Ann Moran
University of Georgia
Univ_Georgia
laboratory