http://lod.bco-dmo.org/id/dataset/671521
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
2016-12-28
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Hemichordata and Echinodermata GenBank accessions, Table S2, Cannon et al (2014) Curr. Bio. (Antarctic Inverts project)
2016-12-22
publication
2016-12-22
revision
BCO-DMO Linked Data URI
2016-12-22
creation
http://lod.bco-dmo.org/id/dataset/671521
Kenneth M. Halanych
Auburn University
principalInvestigator
Andrew Mahon
Central Michigan University
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: Halanych, K. M., Mahon, A. (2016) Hemichordata and Echinodermata GenBank accessions, Table S2, Cannon et al (2014) Curr. Bio. (Antarctic Inverts project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2016-12-22 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/671521 [access date]
Hemichordata and Echinodermata transcriptome NCBI accessions Dataset Description: Methods and Sampling: <p>From Cannon et al 2014):<br />
<strong>Taxon Sampling</strong><br />
We sampled transcriptomic data from representatives of all recognized hemichordate families and all echinoderm classes except Echinoidea, for which data were already available (Tables S1 and S2). At least two species of each taxonomic group were sampled, except for Spengelidae. Samples from which novel transcriptomic data were obtained were collected in various locations, transported live to the laboratory, transferred to RNAlater, frozen at -80C, or kept in ethanol at -20C.</p>
<p><strong>Sequencing and Assembly</strong><br />
Total RNA was extracted from fresh or preserved samples, and cDNA libraries were prepared using the SMART cDNA Library Construction Kit (Clontech; see Supplemental Experimental Procedures for further details). Samples were sequenced with 454 FLX, 454 Titanium, or Illumina HiSeq 2000. Generated sequence data were augmented with publicly available data. Taxa sequenced by 454 or Sanger methods were assembled and processed using the EST2uni pipeline [Forment et al, 2008], while those sequenced by Illumina were digitally normalized using khmer [Brown et al, 2012] and assembled using Trinity [Ebersberger, et al, 2009]. Contigs (for Illumina libraries) or contigs + high-quality singletons (for 454 and Sanger libraries) were translated using TransDecoder (http:// sourceforge.net/projects/transdecoder/). Table S2 provides the number of unigenes (contigs for Illumina libraries and contigs + singletons for 454 and Sanger libraries) obtained for each taxon.</p>
<p>Identification of putative ortholog groups (OGs) was conducted with HaMStR [Ebersberger et al, 2009] using the ‘‘model organisms’’ reference taxon set. After orthology determination, sequences from two 454 libraries from Ophionotusvictoriae and four libraries from Rhabdopleura species were combined into chimeric OTUs in order to reduce the amount of missing data per taxon.</p>
<p>Orthology groups were filtered following the approach of Kocot et al. [2011] First, only sequences greater than 100 aa in length, and OGs with at least 15ambulacrarian taxa and including at least one pterobranch sequence, were retained for further analyses. Sequences less than 100 aa in length were deleted because they are likely to be incorrectly aligned. To remove mistranslated sequence ends, we trimmed amino acid sequences when stop codons (marked by X) were present in either the first or last 20 characters. Each OG was aligned with MAFFT [Katoh et al, 2005] and then trimmed with Aliscore and Alicut [Misof and&nbsp;Misof, 2009] to remove columns with ambiguous alignment.</p>
<p>Next, individual alignments were manually evaluated for partially mistranslated sequences, which were deleted or trimmed as appropriate. Single-OG trees were then constructed for each OG using RAxML v7.3.8 [Stamatakis, 2006] with the PROTGAMMALGF model. Individual gene trees were manually evaluated for sequence contamination as described in Supplemental Experimental Procedures.After manual screening of alignments and individual OG trees, 299 alignments remained, constituting the basis for the 299/33 data set. To screen for potential paralogs, we used PhyloTreePruner [Kocot et al, 2013] (details in Supplemental Experimental Procedures). Alignments passing screening via PhyloTreePruner constituted the 185/33 and 185/31 data sets. To test the effect of low-coverage taxa and missing data on our phylogenetic reconstruction, we employed MARE [Meyer et al, 2010] to generate the 165/20 data set (weighting of information content parameter alpha = 3).</p>
<p><strong>Phylogenetic Analyses</strong><br />
Maximum-likelihood phylogenetic analyses of all data sets were conducted using RAxML v7.7.6 [Stamatakis, 2006] using a PROTGAMMALGF model for each individual OG partition. This model was the most appropriate for the majority of genes and was among the best-fitting models for nearly all OGs as assessed by ProtTest [Darriba et al, 2011]. Previous work [Kocot et al, 2011] and preliminary analyses on these data sets indicated that employing a single model across all partitions recovers highly similar trees while proving considerably less computationally expensive than specifying individual models for all partitions. Nodal support was assessed with 1,000 replicates of nonparametric bootstrapping. Bootstrapped trees from the 185/33 data set were used to calculate leaf stability and taxonomic instability indices of each OTU using the RogueNaRok server (http://rnr.h-its.org). Competing hypotheses ofambulacrarian phylogeny were evaluated using the SH test [Shimodaira, 2002] as implemented in RAxML with the PROTGAMMALGF model for each OG partition. Bayesian inference analyses were conducted using PhyloBayes 2.3 [Lartillot et al, 2013] with the CAT model, which accounts for site specific rate heterogeneity, with two independent chains run for 11,000 cycles each and 1,100 cycles discarded as burn-in. Topology and posterior consensus support was generated using the bpcomp program within PhyloBayes; convergence of the two chains was indicated by ‘‘maxdiff’’ values below 0.2. All phylogenetic analyses were conducted on the Auburn University CASIC HPC supercomputer.</p>
<p><strong>Accession Numbers</strong><br />
Sequence Read Archive (SRA) accession numbers for all data are given in Table S2. The four data matrices are available from the Dryad Digital Repository (http://datadryad.org) with the DOI http://dx.doi.org/10.5061/dryad.20s7c.</p>
Funding provided by NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) Award Number: PLR-1043745 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1043745
Funding provided by NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) Award Number: PLR-1043670 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1043670
onGoing
Kenneth M. Halanych
Auburn University
334-844-3222
101 Life Sciences Building Department of Biological Sciences, Auburn University
Auburn
AL
36849
USA
ken@auburn.edu
pointOfContact
Andrew Mahon
Central Michigan University
989-774-6777
Office of Research & Graduate St
Mount Pleasant
MI
48859-0001
USA
mahon2a@cmich.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
species
taxa_new_to_study
source
num_reads
num_unigenes
HaMStR_OGs
NCBI_accession
link_NCBI_accession
Illumina MiSeq (San Diego, CA) at Auburn University
theme
None, User defined
species scientific name (binomial)
flag
No BCO-DMO term
accession number
external_link
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
NBP1210
Halanych_lab_2011-16
service
Deployment Activity
Ross Sea
laboratory studies
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.
Genetic connectivity and biogeographic patterns of Antarctic benthic invertebrates
https://osprey.bco-dmo.org/project/665837
Genetic connectivity and biogeographic patterns of Antarctic benthic invertebrates
<p><em>Extracted from the NSF award abstract:</em></p>
<p>The research will explore the genetics, diversity, and biogeography of Antarctic marine benthic invertebrates, seeking to overturn the widely accepted suggestion that benthic fauna do not constitute a large, panmictic population. The investigators will sample adults and larvae from undersampled regions of West Antarctica that, combined with existing samples, will provide significant coverage of the western hemisphere of the Southern Ocean. The objectives are: 1) To assess the degree of genetic connectivity (or isolation) of benthic invertebrate species in the Western Antarctic using high-resolution genetic markers. 2) To begin exploring planktonic larvae spatial and bathymetric distributions for benthic shelf invertebrates in the Bellinghausen, Amundsen and Ross Seas. 3) To continue to develop a Marine Antarctic Genetic Inventory (MAGI) that relates larval and adult forms via DNA barcoding. </p>
Antarctic Inverts
largerWorkCitation
project
eng; USA
biota
oceans
Ross Sea; laboratory studies
2001-01-01
2013-12-31
Antarctica
0
BCO-DMO catalogue of parameters from Hemichordata and Echinodermata GenBank accessions, Table S2, Cannon et al (2014) Curr. Bio. (Antarctic Inverts 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/671541.rdf
Name: species
Units: unitless
Description: <p>taxonomic genus and species name</p>
http://lod.bco-dmo.org/id/dataset-parameter/671542.rdf
Name: taxa_new_to_study
Units: unitless
Description: <p>whether these are new sequences for this study</p>
http://lod.bco-dmo.org/id/dataset-parameter/671543.rdf
Name: source
Units: unitless
Description: <p>genomics services lab and instrument</p>
http://lod.bco-dmo.org/id/dataset-parameter/671544.rdf
Name: num_reads
Units: reads
Description: <p>number of reads</p>
http://lod.bco-dmo.org/id/dataset-parameter/671545.rdf
Name: num_unigenes
Units: genes
Description: <p>number of uni-genes (contigs for Illumina libraries and contigs + singletons for 454 and Sanger libraries) obtained for each taxon</p>
http://lod.bco-dmo.org/id/dataset-parameter/671546.rdf
Name: HaMStR_OGs
Units: unitless
Description: <p>???orthologous genes from HaMStr profile</p>
http://lod.bco-dmo.org/id/dataset-parameter/671547.rdf
Name: NCBI_accession
Units: unitless
Description: <p>NCBI GenBank accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/671548.rdf
Name: link_NCBI_accession
Units: unitless
Description: <p>link to GenBank accession page</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
7694
https://datadocs.bco-dmo.org/file/0AAMNRQUgjVQ7O/Cannon_2014_TS2.csv
Cannon_2014_TS2.csv
Primary data file for dataset ID 671521
download
https://osprey.bco-dmo.org/dataset/671521/data/download
download
onLine
dataset
<p>From Cannon et al 2014):<br />
<strong>Taxon Sampling</strong><br />
We sampled transcriptomic data from representatives of all recognized hemichordate families and all echinoderm classes except Echinoidea, for which data were already available (Tables S1 and S2). At least two species of each taxonomic group were sampled, except for Spengelidae. Samples from which novel transcriptomic data were obtained were collected in various locations, transported live to the laboratory, transferred to RNAlater, frozen at -80C, or kept in ethanol at -20C.</p>
<p><strong>Sequencing and Assembly</strong><br />
Total RNA was extracted from fresh or preserved samples, and cDNA libraries were prepared using the SMART cDNA Library Construction Kit (Clontech; see Supplemental Experimental Procedures for further details). Samples were sequenced with 454 FLX, 454 Titanium, or Illumina HiSeq 2000. Generated sequence data were augmented with publicly available data. Taxa sequenced by 454 or Sanger methods were assembled and processed using the EST2uni pipeline [Forment et al, 2008], while those sequenced by Illumina were digitally normalized using khmer [Brown et al, 2012] and assembled using Trinity [Ebersberger, et al, 2009]. Contigs (for Illumina libraries) or contigs + high-quality singletons (for 454 and Sanger libraries) were translated using TransDecoder (http:// sourceforge.net/projects/transdecoder/). Table S2 provides the number of unigenes (contigs for Illumina libraries and contigs + singletons for 454 and Sanger libraries) obtained for each taxon.</p>
<p>Identification of putative ortholog groups (OGs) was conducted with HaMStR [Ebersberger et al, 2009] using the ‘‘model organisms’’ reference taxon set. After orthology determination, sequences from two 454 libraries from Ophionotusvictoriae and four libraries from Rhabdopleura species were combined into chimeric OTUs in order to reduce the amount of missing data per taxon.</p>
<p>Orthology groups were filtered following the approach of Kocot et al. [2011] First, only sequences greater than 100 aa in length, and OGs with at least 15ambulacrarian taxa and including at least one pterobranch sequence, were retained for further analyses. Sequences less than 100 aa in length were deleted because they are likely to be incorrectly aligned. To remove mistranslated sequence ends, we trimmed amino acid sequences when stop codons (marked by X) were present in either the first or last 20 characters. Each OG was aligned with MAFFT [Katoh et al, 2005] and then trimmed with Aliscore and Alicut [Misof and&nbsp;Misof, 2009] to remove columns with ambiguous alignment.</p>
<p>Next, individual alignments were manually evaluated for partially mistranslated sequences, which were deleted or trimmed as appropriate. Single-OG trees were then constructed for each OG using RAxML v7.3.8 [Stamatakis, 2006] with the PROTGAMMALGF model. Individual gene trees were manually evaluated for sequence contamination as described in Supplemental Experimental Procedures.After manual screening of alignments and individual OG trees, 299 alignments remained, constituting the basis for the 299/33 data set. To screen for potential paralogs, we used PhyloTreePruner [Kocot et al, 2013] (details in Supplemental Experimental Procedures). Alignments passing screening via PhyloTreePruner constituted the 185/33 and 185/31 data sets. To test the effect of low-coverage taxa and missing data on our phylogenetic reconstruction, we employed MARE [Meyer et al, 2010] to generate the 165/20 data set (weighting of information content parameter alpha = 3).</p>
<p><strong>Phylogenetic Analyses</strong><br />
Maximum-likelihood phylogenetic analyses of all data sets were conducted using RAxML v7.7.6 [Stamatakis, 2006] using a PROTGAMMALGF model for each individual OG partition. This model was the most appropriate for the majority of genes and was among the best-fitting models for nearly all OGs as assessed by ProtTest [Darriba et al, 2011]. Previous work [Kocot et al, 2011] and preliminary analyses on these data sets indicated that employing a single model across all partitions recovers highly similar trees while proving considerably less computationally expensive than specifying individual models for all partitions. Nodal support was assessed with 1,000 replicates of nonparametric bootstrapping. Bootstrapped trees from the 185/33 data set were used to calculate leaf stability and taxonomic instability indices of each OTU using the RogueNaRok server (http://rnr.h-its.org). Competing hypotheses ofambulacrarian phylogeny were evaluated using the SH test [Shimodaira, 2002] as implemented in RAxML with the PROTGAMMALGF model for each OG partition. Bayesian inference analyses were conducted using PhyloBayes 2.3 [Lartillot et al, 2013] with the CAT model, which accounts for site specific rate heterogeneity, with two independent chains run for 11,000 cycles each and 1,100 cycles discarded as burn-in. Topology and posterior consensus support was generated using the bpcomp program within PhyloBayes; convergence of the two chains was indicated by ‘‘maxdiff’’ values below 0.2. All phylogenetic analyses were conducted on the Auburn University CASIC HPC supercomputer.</p>
<p><strong>Accession Numbers</strong><br />
Sequence Read Archive (SRA) accession numbers for all data are given in Table S2. The four data matrices are available from the Dryad Digital Repository (http://datadryad.org) with the DOI http://dx.doi.org/10.5061/dryad.20s7c.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing notes:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- added links to NCBI accession pages</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 (San Diego, CA) at Auburn University
Illumina MiSeq (San Diego, CA) at Auburn University
PI Supplied Instrument Name: Illumina MiSeq (San Diego, CA) at Auburn University 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)
Cruise: NBP1210
NBP1210
Community Standard Description
International Council for the Exploration of the Sea
RVIB Nathaniel B. Palmer
vessel
NBP1210
Kenneth M. Halanych
Auburn University
http://dmoserv3.bco-dmo.org/jg/serv/BCO-DMO/OA_Antarctic_organisms/727518.html0%7Bdir=dmoserv3.whoi.edu/jg/dir/BCO-DMO/OA_Antarctic_organisms/,info=dmoserv3.bco-dmo.org/jg/info/BCO-DMO/OA_Antarctic_organisms/mg_ca_ratios%7D
Report describing NBP1210
Deployment: Halanych_lab_2011-16
Halanych_lab_2011-16
Auburn University lab
laboratory
Halanych_lab_2011-16
Kenneth M. Halanych
Auburn University
Community Standard Description
International Council for the Exploration of the Sea
RVIB Nathaniel B. Palmer
vessel