http://lod.bco-dmo.org/id/dataset/626566
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
2015-11-16
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Planktonic ciliate DNA sequence GenBank accession numbers for samples collected on the R/V Cape Hatteras (CH0112) cruise in the NW Atlantic Continental Shelf during 2015 (CiliateSequencing project)
2015-11-18
publication
2015-11-18
revision
BCO-DMO Linked Data URI
2015-11-18
creation
http://lod.bco-dmo.org/id/dataset/626566
George McManus
University of Connecticut
principalInvestigator
Laura A. Katz
Smith College
principalInvestigator
Luciana Santoferrara
University of Connecticut
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: McManus, G., Katz, L. A., Santoferrara, L. (2015) Planktonic ciliate DNA sequence GenBank accession numbers for samples collected on the R/V Cape Hatteras (CH0112) cruise in the NW Atlantic Continental Shelf during 2015 (CiliateSequencing project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2015-11-18) Version Date 2015-11-18 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/626566 [access date]
Planktonic ciliate DNA sequence accession numbers at NCBI GenBank Dataset Description: <p>This dataset includes 4 sets of NCBI accession numbers for planktonic ciliates. Some of the links to the NCBI pages are not yet live.</p>
<p>Contact for the single cells from Long Island Sound:&nbsp;Luciana Santoferrara, post-doc: luciana.santoferrara_at_uconn.edu. Contact for the other data: George McManus.</p> Methods and Sampling: <p><strong>DGGE_Weiker: </strong>&nbsp;Surface samples were collected while following a surface drifter (crosse window shade type). DNA was extracted and amplified with PCR, and amplicons were separated with denaturant gradient gel electrophoresis.&nbsp; Sequencing use the Sanger method. Details can be found in Grattepanche, et al, 2014.</p>
<p><strong>454 Long Island Sound:</strong> Surface and deep samples were taken from the Sound on several occasions. DNA was extracted and a ciliate clade-specific portion of the small subunit ribosomal gene was amplified using the polymerase chain reaction. Amplified fragments were sequenced using the Roche 454 platform.&nbsp; Details are reported in Santoferrara, et al, 2014.</p>
<p><strong>454 and DGGE Hatteras:</strong> Vertically-resolved samples were collected along a section due south from Naragansett RI to the shelf break. DNA was extracted and amplified with PCR, and amplicons were separated with denaturant gradient gel electrophoresis or sequenced with Roche 454. Methodological details can be found in Grattepanche, et al, 2014 and&nbsp;Santoferrara, et al, 2014.</p>
<p><strong>Single cells, Long Island Sound:</strong> Individual cells of tintinnid microzooplankton were picked with a micropipette, photo documented and placed in buffer for extraction and sequencing. Sequences of the internal transcribed spacer regions (ITS1-5.8S-ITS2), the small sub unit ribosomal gene (SSU), and the large subunit ribosomal gene (LSU) were obtained by Sanger sequencing.</p>
<p><strong>References:</strong></p>
<p>Grattepanche, J-D, L Santoferrara, J Andrade, AM Oliverio, GB McManus, and LA Katz. 2014. Distribution and diversity of oligotrich and choreotrich ciliates assessed by morphology and by DGGE in temperate coastal waters. Aquat. Microb. Ecol. 71:211-221. DOI:10.3354/ame01675.</p>
<p>Santoferrara, L, J-D Grattepanche, LA Katz, and GB McManus. 2014. Pyrosequencing for assessing diversity of eukaryotic microbes: analysis of data on marine planktonic ciliates and comparison with traditional methods. Environ. Microbiol. DOI:&nbsp;10.1111/1462-2920.12380.</p>
<p>Santoferrara, LF, GB McManus, and VA Alder. 2012. Utility of Genetic Markers and Morphology for Species Discrimination within the Order Tintinnida (Ciliophora, Spirotrichea). Protist , doi:10.1016/j.protis.2011.12.002</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1130033 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1130033
onGoing
George McManus
University of Connecticut
860-405-8602
Department of Marine Sciences, University of Connecticut 1080 Shennecossett Rd.
Groton
CT
06340
USA
george.mcmanus@uconn.edu
pointOfContact
Laura A. Katz
Smith College
413-585-3825
Department of Biological Sciences Smith College Burton Hall 201
Northampton
MA
01063
USA
lkatz@smith.edu
pointOfContact
Luciana Santoferrara
University of Connecticut
516-463-7718
Biology Dept Room 301 Gittleson Hall
Hempstead
NY
11549-1000
USA
luciana.santoferrara@hofstra.edu
pointOfContact
asNeeded
Dataset Version: 2015-11-18
Unknown
dataset_id
location
lat
lon
cruise_id
date
description
comment
NCBI_accession
theme
None, User defined
dataset_id
site
latitude
longitude
Cruise identfier
date
No BCO-DMO term
comments
accession number
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
UConn_McManus_2015
CH0112
service
Deployment Activity
Avery Point, Connecticut
NW Atlantic Continental Shelf
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.
Diversity and dynamics of planktonic ciliates - what can next-generation sequencing technologies tell us?
http://microzooplankton.uconn.edu
Diversity and dynamics of planktonic ciliates - what can next-generation sequencing technologies tell us?
<p>The Ocean's biomass and diversity are predominantly microbial, yet this aspect of diversity remains underexplored. Efforts in recent years have begun to document microbial diversity in marine systems, and to elucidate the processes that structure assemblages across space and time. This project focuses on two important sister clades of microbial eukaryotes, the oligotrich and choreotrich ciliates. These organisms comprise a major component of planktonic food webs as they graze on phytoplankton, and are in turn eaten by zooplankton and larval fish.</p>
<p>Earlier molecular work on ciliate diversity relied on light microscopy, construction of clone libraries and Sanger sequencing. This revealed a high degree of cryptic diversity (similar species that are genetically distinct), which is surprising, given the long-held idea that all microbes are globally distributed and that few species exist, at least as compared to animals and plants. This past work also showed that ciliate assemblages contain a few highly abundant forms and many rare ones, consistent with the concept of a "rare biosphere". However, these methods are limited by high costs of both labor and materials, so that efforts to sample any local assemblage comprehensively usually resulted in undersaturation (repeated sampling continued to uncover new species). Next generation approaches are needed to truly assess the depths of biodiversity in planktonic ciliates.</p>
<p>This project brings together investigators with strengths in ecology, taxonomy and oceanography (PI McManus) and in molecular evolution, systematics and bioinformatics (PI Katz). Pyrosequencing will be used to sample the oligotrich and choreotrich ciliates ’to exhaustion’ in coastal environments. Denaturing gradient gel electrophoresis (DGGE), a technique that generates a fingerprint of the diversity in a sample, will be used to pre-select samples for pyrosequencing based on where strong gradients are observed in the composition of assemblages in relation to environmental factors (density fronts, thermolclines, etc.). Using these approaches, combined with the informatics pipeline already in place, this project will address three specific objectives:</p>
<p><strong>Objective 1.</strong> Determine the spatial scale of variability in ciliate diversity by measuring how ciliate assemblages change over meter, kilometer, 100 km, and basin scales.</p>
<p><strong>Objective 2.</strong> Assess the contributions of different size classes of ciliates to overall assemblage diversity.</p>
<p><strong>Objective 3.</strong> Experimentally evaluate factors that control the temporal shift of individual species from rarity to commonness in a natural assemblage, and vice versa.</p>
<p>Note: See the related collaborative project, "<a href="http://www.bco-dmo.org/project/560529">Patterns of diversity in planktonic ciliates: spatio-temporal scales and community assembly in the coastal ocean</a>", funded by awards OCE-1435515 and OCE-1436003.</p>
CiliateSequencing
largerWorkCitation
project
eng; USA
biota
oceans
Avery Point, Connecticut; NW Atlantic Continental Shelf
2015-11-18
NW Atlantic Continental Shelf
0
BCO-DMO catalogue of parameters from Planktonic ciliate DNA sequence GenBank accession numbers for samples collected on the R/V Cape Hatteras (CH0112) cruise in the NW Atlantic Continental Shelf during 2015 (CiliateSequencing 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/626669.rdf
Name: dataset_id
Units: unitless
Description: <p>name of dataset</p>
http://lod.bco-dmo.org/id/dataset-parameter/626670.rdf
Name: location
Units: unitless
Description: <p>location of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/626671.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/626672.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/626673.rdf
Name: cruise_id
Units: unitless
Description: <p>cruise identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/626674.rdf
Name: date
Units: yyyy-mm-dd
Description: <p>date of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/626675.rdf
Name: description
Units: unitless
Description: <p>DGGE: Denaturing Gradient Gel Electrophoresis; ITS: Internal Transcribed Spacer region of the ribosomal gene (ITS1-5.8S-ITS2); SSU: Small Sub-Unit of the ribosomal gene; LSU: Large Sub-Unit of the ribosomal gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/626676.rdf
Name: comment
Units: unitless
Description: <p>comment</p>
http://lod.bco-dmo.org/id/dataset-parameter/626677.rdf
Name: NCBI_accession
Units: unitless
Description: <p>NCBI accession number</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
55716
https://datadocs.bco-dmo.org/file/933jznAsm3BXVK/ciliate_accessions.csv
ciliate_accessions.csv
Primary data file for dataset ID 626566
download
https://osprey.bco-dmo.org/dataset/626566/data/download
download
onLine
dataset
<p><strong>DGGE_Weiker: </strong>&nbsp;Surface samples were collected while following a surface drifter (crosse window shade type). DNA was extracted and amplified with PCR, and amplicons were separated with denaturant gradient gel electrophoresis.&nbsp; Sequencing use the Sanger method. Details can be found in Grattepanche, et al, 2014.</p>
<p><strong>454 Long Island Sound:</strong> Surface and deep samples were taken from the Sound on several occasions. DNA was extracted and a ciliate clade-specific portion of the small subunit ribosomal gene was amplified using the polymerase chain reaction. Amplified fragments were sequenced using the Roche 454 platform.&nbsp; Details are reported in Santoferrara, et al, 2014.</p>
<p><strong>454 and DGGE Hatteras:</strong> Vertically-resolved samples were collected along a section due south from Naragansett RI to the shelf break. DNA was extracted and amplified with PCR, and amplicons were separated with denaturant gradient gel electrophoresis or sequenced with Roche 454. Methodological details can be found in Grattepanche, et al, 2014 and&nbsp;Santoferrara, et al, 2014.</p>
<p><strong>Single cells, Long Island Sound:</strong> Individual cells of tintinnid microzooplankton were picked with a micropipette, photo documented and placed in buffer for extraction and sequencing. Sequences of the internal transcribed spacer regions (ITS1-5.8S-ITS2), the small sub unit ribosomal gene (SSU), and the large subunit ribosomal gene (LSU) were obtained by Sanger sequencing.</p>
<p><strong>References:</strong></p>
<p>Grattepanche, J-D, L Santoferrara, J Andrade, AM Oliverio, GB McManus, and LA Katz. 2014. Distribution and diversity of oligotrich and choreotrich ciliates assessed by morphology and by DGGE in temperate coastal waters. Aquat. Microb. Ecol. 71:211-221. DOI:10.3354/ame01675.</p>
<p>Santoferrara, L, J-D Grattepanche, LA Katz, and GB McManus. 2014. Pyrosequencing for assessing diversity of eukaryotic microbes: analysis of data on marine planktonic ciliates and comparison with traditional methods. Environ. Microbiol. DOI:&nbsp;10.1111/1462-2920.12380.</p>
<p>Santoferrara, LF, GB McManus, and VA Alder. 2012. Utility of Genetic Markers and Morphology for Species Discrimination within the Order Tintinnida (Ciliophora, Spirotrichea). Protist , doi:10.1016/j.protis.2011.12.002</p>
Specified by the Principal Investigator(s)
<p><strong>DGGE_Weiker:</strong> Raw chromatograms were checked by eye and fragments were assembled into contains using LaserGene.</p>
<p><strong>454 Long Island Sound:</strong> Sequences were processed in QIIME using a quality score of 37 without clustering.</p>
<p><strong>454 and DGGE Hatteras: </strong>For DGGE, raw chromatograms were checked by eye and fragments were assembled into contains using LaserGene. For 454 data, sequences were processed in QIIME using a quality score of 37 and without clustering.</p>
<p><strong>Single cells, Long Island Sound:</strong> Raw chromatograms were edited by eye and contains were assembled using MEGA. Details can be found in Santoferrara, et al, 2012.</p>
<p><strong>BCO-DMO Processing:</strong><br />
- Created&nbsp;a&nbsp;table&nbsp;with&nbsp;columns:&nbsp;dataset_id, location, lat, lon, cruise_id, date, description,&nbsp;comment, accession_number.<br />
- Created links to the accessions.&nbsp;</p>
<p>&nbsp;</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
PI Supplied Instrument Name: PI Supplied Instrument Description:Roche 454 platform and others 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: 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)
Deployment: UConn_McManus_2015
UConn_McManus_2015
Univ_Connecticut
laboratory
Cruise: CH0112
CH0112
R/V Cape Hatteras
Community Standard Description
International Council for the Exploration of the Sea
R/V Cape Hatteras
vessel
CH0112
George McManus
University of Connecticut
Univ_Connecticut
laboratory
R/V Cape Hatteras
Community Standard Description
International Council for the Exploration of the Sea
R/V Cape Hatteras
vessel