{"@context":{"content":"http:\/\/purl.org\/rss\/1.0\/modules\/content\/","dc":"http:\/\/purl.org\/dc\/terms\/","foaf":"http:\/\/xmlns.com\/foaf\/0.1\/","og":"http:\/\/ogp.me\/ns#","rdfs":"http:\/\/www.w3.org\/2000\/01\/rdf-schema#","sioc":"http:\/\/rdfs.org\/sioc\/ns#","sioct":"http:\/\/rdfs.org\/sioc\/types#","skos":"http:\/\/www.w3.org\/2004\/02\/skos\/core#","xsd":"http:\/\/www.w3.org\/2001\/XMLSchema#","owl":"http:\/\/www.w3.org\/2002\/07\/owl#","rdf":"http:\/\/www.w3.org\/1999\/02\/22-rdf-syntax-ns#","rss":"http:\/\/purl.org\/rss\/1.0\/","site":"https:\/\/www.bco-dmo.org\/ns#","odo":"http:\/\/ocean-data.org\/schema\/","emo":"http:\/\/ocean-data.org\/schema\/entity-matching#","bibo":"http:\/\/purl.org\/ontology\/bibo\/","crypto":"http:\/\/id.loc.gov\/vocabulary\/preservation\/cryptographicHashFunctions\/","bcodmo":"http:\/\/lod.bco-dmo.org\/id\/","tw":"http:\/\/tw.rpi.edu\/schema\/","dcat":"http:\/\/www.w3.org\/ns\/dcat#","time":"http:\/\/www.w3.org\/2006\/time#","geo":"http:\/\/www.w3.org\/2003\/01\/geo\/wgs84_pos#","geosparql":"http:\/\/www.opengis.net\/ont\/geosparql#","sf":"http:\/\/www.opengis.net\/ont\/sf#","void":"http:\/\/rdfs.org\/ns\/void#","sd":"http:\/\/www.w3.org\/ns\/sparql-service-description#","dctype":"http:\/\/purl.org\/dc\/dcmitype\/","prov":"http:\/\/www.w3.org\/ns\/prov#","schema":"http:\/\/schema.org\/","geolink":"http:\/\/schema.geolink.org\/1.0\/base\/main#","spdx":"http:\/\/spdx.org\/rdf\/terms#","bcodmo_vocab":"http:\/\/schema.bco-dmo.org\/"},"@id":"http:\/\/lod.bco-dmo.org\/id\/dataset\/471914#graph","@graph":[{"http:\/\/lod.bco-dmo.org\/id\/dataset\/471914":{"@id":"http:\/\/lod.bco-dmo.org\/id\/dataset\/471914","@type":["http:\/\/ocean-data.org\/schema\/DeploymentDatasetCollection","http:\/\/www.w3.org\/ns\/dcat#Dataset","http:\/\/ocean-data.org\/schema\/Dataset"],"http:\/\/ocean-data.org\/schema\/hasAcquisitionDescription":[{"@value":"
\u00a0Wildtype and mutant ryhB strains of ES114 were grown in Aquil media with glucose and NH4 as carbon and nitrogen sources, respectively. Parallel cultures of each strain were resuspended in media containing low iron and followed until the growth rates decreased. At this point, samples for RNA were collected by filtration, stored in RNAlater and later extracted using standard methods. rRNA depleted cDNA libraries were submitted to UGA\u2019s Georgia Genomics Center for sequencing on an Illumina MiSeq instrument.<\/p><\/div>","@type":"rdf:HTML"}],"http:\/\/ocean-data.org\/schema\/hasBriefDescription":[{"@value":"Predicted regulon of the regulatory RNA ryhB in Vibrio fischeri","@language":"en-US"}],"http:\/\/purl.org\/dc\/terms\/description":[{"@value":"
An RNA-Seq experiment was performed in order to define the regulon of the small, regulatory RNA RyhB in Vibrio fischeri ES114. This was done by comparing the global gene expression in wildtype and ryhB mutant strains of V. fischeri. Since RyhB is de-repressed only under iron limiting conditions, this comparison must be performed when the level of intracellular iron is low.<\/p><\/div>","@type":"rdf:HTML"}],"http:\/\/www.w3.org\/2000\/01\/rdf-schema#label":[{"@value":"RNASeq Exp5","@type":"xsd:string"}],"http:\/\/ocean-data.org\/schema\/hasProcessingDescription":[{"@value":"
Base quality and trimming of reads was assessed using the FastX-Toolkit v0.0.13.2, only reads above a Q30 value were retained. Reads were mapped back to the Vibrio fischeri reference genome using TopHat v1.2.0. Expressed genes and transcripts were assembled for each replicate culture separately using Cufflinks v2.1.1. Cuffmerge v.2.1.1 was then utilized to merge all assemblies from the wildtype and ryhB mutant cultures, respectively. Finally, differentially expressed genes were identified using Cuffdiff v2.1.1.<\/p>\n
\u00a0<\/p><\/div>","@type":"rdf:HTML"}],"http:\/\/purl.org\/dc\/terms\/identifier":[{"@value":"471914","@type":"xsd:int"}],"http:\/\/purl.org\/dc\/terms\/title":[{"@value":"RNASeq Exp5"}],"http:\/\/purl.org\/dc\/terms\/date":[{"@value":"2013-11-21T15:12:33-05:00","@type":"xsd:dateTime"}],"http:\/\/purl.org\/dc\/terms\/created":[{"@value":"2013-11-21T15:12:33-05:00","@type":"xsd:dateTime"}],"http:\/\/purl.org\/dc\/terms\/modified":[{"@value":"2023-07-07T16:10:26-04:00","@type":"xsd:dateTime"}],"http:\/\/rdfs.org\/ns\/void#inDataset":[{"@id":"http:\/\/www.bco-dmo.org\/"}],"http:\/\/ocean-data.org\/schema\/namedGraph":[{"@value":"urn:bcodmo:dataset:471914","@type":"xsd:token"}],"http:\/\/ocean-data.org\/schema\/osprey_page":[{"@id":"https:\/\/www.bco-dmo.org\/dataset\/471914"}],"http:\/\/ocean-data.org\/schema\/identifier":[{"@value":"_:Identifier471914"}],"http:\/\/ocean-data.org\/schema\/datasetTitle":[{"@value":"Predicted regulon of the regulatory RNA ryhB in Vibrio fischeri (Iron regulation in Vibrio project)","@language":"en-US"}],"http:\/\/ocean-data.org\/schema\/abstract":[{"@value":"","@language":"en-US"}],"http:\/\/purl.org\/dc\/terms\/rights":[{"@id":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"http:\/\/ocean-data.org\/schema\/deprecated":[{"@value":"false","@type":"xsd:boolean"}],"http:\/\/purl.org\/dc\/terms\/bibliographicCitation":[{"@value":"Mann, E., Stabb, E., Voit, E. (2013) Predicted regulon of the regulatory RNA ryhB in Vibrio fischeri (Iron regulation in Vibrio project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2013-11-21 [if applicable, indicate subset used]. http:\/\/lod.bco-dmo.org\/id\/dataset\/471914 [access date]","@type":"xsd:string"}],"http:\/\/ocean-data.org\/schema\/validated":[{"@value":"true","@type":"xsd:boolean"}],"http:\/\/ocean-data.org\/schema\/currentState":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/dataset-current-state\/7"}],"http:\/\/ocean-data.org\/schema\/nodcTopic":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/nodc-dataset-topic\/156"}],"http:\/\/ocean-data.org\/schema\/restricted":[{"@value":"false","@type":"xsd:boolean"}],"http:\/\/ocean-data.org\/schema\/hasAward":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/award\/471906"}],"http:\/\/ocean-data.org\/schema\/fromInstrument":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/dataset-instrument\/471917"}],"http:\/\/ocean-data.org\/schema\/storesValuesFor":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/dataset-parameter\/471968"},{"@id":"http:\/\/lod.bco-dmo.org\/id\/dataset-parameter\/471969"},{"@id":"http:\/\/lod.bco-dmo.org\/id\/dataset-parameter\/471970"},{"@id":"http:\/\/lod.bco-dmo.org\/id\/dataset-parameter\/471971"},{"@id":"http:\/\/lod.bco-dmo.org\/id\/dataset-parameter\/471972"},{"@id":"http:\/\/lod.bco-dmo.org\/id\/dataset-parameter\/471973"},{"@id":"http:\/\/lod.bco-dmo.org\/id\/dataset-parameter\/471974"},{"@id":"http:\/\/lod.bco-dmo.org\/id\/dataset-parameter\/471975"},{"@id":"http:\/\/lod.bco-dmo.org\/id\/dataset-parameter\/471976"}],"http:\/\/ocean-data.org\/schema\/hasAgentWithRole":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/person-role\/471918"},{"@id":"http:\/\/lod.bco-dmo.org\/id\/person-role\/471919"},{"@id":"http:\/\/lod.bco-dmo.org\/id\/person-role\/471920"},{"@id":"http:\/\/lod.bco-dmo.org\/id\/person-role\/471921"}],"http:\/\/purl.org\/dc\/terms\/language":[{"@value":"http:\/\/id.loc.gov\/vocabulary\/iso639-1\/en","@type":"xsd:anyURI"}],"http:\/\/xmlns.com\/foaf\/0.1\/homepage":[{"@id":"https:\/\/www.bco-dmo.org\/dataset\/471914"}],"http:\/\/purl.org\/dc\/terms\/issued":[{"@value":"2013-11-21","@type":"xsd:date"}],"http:\/\/purl.org\/dc\/terms\/publisher":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/affiliation\/191"}],"http:\/\/www.w3.org\/ns\/dcat#contactPoint":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/person\/471908"}]},"_:html471914":{"@id":"_:html471914","@type":["http:\/\/ocean-data.org\/schema\/MetadataViewAffordance"],"http:\/\/schema.org\/subjectOf":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/dataset\/471914"}],"http:\/\/schema.org\/name":[{"@value":"HTML","@type":"xsd:string"}],"http:\/\/ocean-data.org\/schema\/affordedBy":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/affiliation\/191"}],"http:\/\/schema.org\/target":[{"@value":"_:html471914entryPoint"}]},"_:html471914entryPoint":{"@id":"_:html471914entryPoint","@type":["http:\/\/schema.org\/EntryPoint","http:\/\/ocean-data.org\/schema\/HtmlLandingPage"],"http:\/\/schema.org\/url":[{"@value":"https:\/\/www.bco-dmo.org\/dataset\/471914","@type":"xsd:anyURI"}],"http:\/\/schema.org\/contentType":[{"@value":"text\/html","@type":"xsd:token"}]},"_:frictionlessdata471914":{"@id":"_:frictionlessdata471914","@type":["http:\/\/ocean-data.org\/schema\/MetadataDownloadAffordance"],"http:\/\/schema.org\/subjectOf":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/dataset\/471914"}],"http:\/\/schema.org\/name":[{"@value":"Datapackage.json","@type":"xsd:string"}],"http:\/\/schema.org\/alternateName":[{"@value":"Frictionless Data Package","@type":"xsd:string"}],"http:\/\/ocean-data.org\/schema\/affordedBy":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/affiliation\/191"}],"http:\/\/schema.org\/target":[{"@value":"_:frictionlessdata471914entryPoint"}]},"_:frictionlessdata471914entryPoint":{"@id":"_:frictionlessdata471914entryPoint","@type":["http:\/\/schema.org\/EntryPoint"],"http:\/\/schema.org\/url":[{"@value":"https:\/\/www.bco-dmo.org\/dataset\/471914\/datapackage.json","@type":"xsd:anyURI"}],"http:\/\/schema.org\/contentType":[{"@value":"application\/vnd.datapackage+json","@type":"xsd:token"}]},"_:datasetdescription471914":{"@id":"_:datasetdescription471914","@type":["http:\/\/ocean-data.org\/schema\/MetadataDownloadAffordance"],"http:\/\/schema.org\/subjectOf":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/dataset\/471914"}],"http:\/\/schema.org\/name":[{"@value":"PDF","@type":"xsd:string"}],"http:\/\/ocean-data.org\/schema\/affordedBy":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/affiliation\/191"}],"http:\/\/schema.org\/target":[{"@value":"_:datasetdescription471914entryPoint"}]},"_:datasetdescription471914entryPoint":{"@id":"_:datasetdescription471914entryPoint","@type":["http:\/\/schema.org\/EntryPoint","http:\/\/ocean-data.org\/schema\/PdfDatasetDescription"],"http:\/\/schema.org\/url":[{"@value":"https:\/\/www.bco-dmo.org\/dataset\/471914\/Dataset_description.pdf","@type":"xsd:anyURI"}],"http:\/\/schema.org\/contentType":[{"@value":"application\/pdf","@type":"xsd:token"}]},"_:json471914":{"@id":"_:json471914","@type":["http:\/\/ocean-data.org\/schema\/MetadataDownloadAffordance"],"http:\/\/schema.org\/subjectOf":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/dataset\/471914"}],"http:\/\/schema.org\/name":[{"@value":"JSON-LD","@type":"xsd:string"}],"http:\/\/ocean-data.org\/schema\/affordedBy":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/affiliation\/191"}],"http:\/\/schema.org\/target":[{"@value":"_:json471914entryPoint"}]},"_:json471914entryPoint":{"@id":"_:json471914entryPoint","@type":["http:\/\/schema.org\/EntryPoint"],"http:\/\/schema.org\/url":[{"@value":"https:\/\/www.bco-dmo.org\/dataset\/471914.json","@type":"xsd:anyURI"}],"http:\/\/schema.org\/contentType":[{"@value":"application\/ld+json","@type":"xsd:token"}]},"_:ttl471914":{"@id":"_:ttl471914","@type":["http:\/\/ocean-data.org\/schema\/MetadataDownloadAffordance"],"http:\/\/schema.org\/subjectOf":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/dataset\/471914"}],"http:\/\/schema.org\/name":[{"@value":"Turtle","@type":"xsd:string"}],"http:\/\/ocean-data.org\/schema\/affordedBy":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/affiliation\/191"}],"http:\/\/schema.org\/target":[{"@value":"_:ttl471914entryPoint"}]},"_:ttl471914entryPoint":{"@id":"_:ttl471914entryPoint","@type":["http:\/\/schema.org\/EntryPoint"],"http:\/\/schema.org\/url":[{"@value":"https:\/\/www.bco-dmo.org\/dataset\/471914.ttl","@type":"xsd:anyURI"}],"http:\/\/schema.org\/contentType":[{"@value":"text\/turtle","@type":"xsd:token"}]},"_:rdf471914":{"@id":"_:rdf471914","@type":["http:\/\/ocean-data.org\/schema\/MetadataDownloadAffordance"],"http:\/\/schema.org\/subjectOf":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/dataset\/471914"}],"http:\/\/schema.org\/name":[{"@value":"RDF\/XML","@type":"xsd:string"}],"http:\/\/ocean-data.org\/schema\/affordedBy":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/affiliation\/191"}],"http:\/\/schema.org\/target":[{"@value":"_:rdf471914entryPoint"}]},"_:rdf471914entryPoint":{"@id":"_:rdf471914entryPoint","@type":["http:\/\/schema.org\/EntryPoint"],"http:\/\/schema.org\/url":[{"@value":"https:\/\/www.bco-dmo.org\/dataset\/471914.rdf","@type":"xsd:anyURI"}],"http:\/\/schema.org\/contentType":[{"@value":"application\/rdf+xml","@type":"xsd:token"}]},"_:iso471914":{"@id":"_:iso471914","@type":["http:\/\/ocean-data.org\/schema\/MetadataDownloadAffordance"],"http:\/\/schema.org\/subjectOf":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/dataset\/471914"}],"http:\/\/schema.org\/name":[{"@value":"ISO 19115-2 (NOAA Profile)","@type":"xsd:string"}],"http:\/\/ocean-data.org\/schema\/affordedBy":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/affiliation\/191"}],"http:\/\/schema.org\/target":[{"@value":"_:iso471914entryPoint"}]},"_:iso471914entryPoint":{"@id":"_:iso471914entryPoint","@type":["http:\/\/schema.org\/EntryPoint","http:\/\/ocean-data.org\/schema\/ISOMetadata"],"http:\/\/schema.org\/url":[{"@value":"https:\/\/www.bco-dmo.org\/dataset\/471914\/iso","@type":"xsd:anyURI"}],"http:\/\/schema.org\/contentType":[{"@value":"application\/xml","@type":"xsd:token"}],"http:\/\/purl.org\/dc\/terms\/conformsTo":[{"@value":"http:\/\/www.isotc211.org\/2005\/gmd-noaa","@type":"xsd:anyURI"}]},"_:dublincore471914":{"@id":"_:dublincore471914","@type":["http:\/\/ocean-data.org\/schema\/MetadataDownloadAffordance"],"http:\/\/schema.org\/subjectOf":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/dataset\/471914"}],"http:\/\/schema.org\/name":[{"@value":"Dublin Core","@type":"xsd:string"}],"http:\/\/ocean-data.org\/schema\/affordedBy":[{"@id":"http:\/\/lod.bco-dmo.org\/id\/affiliation\/191"}],"http:\/\/schema.org\/target":[{"@value":"_:dublincore471914entryPoint"}]},"_:dublincore471914entryPoint":{"@id":"_:dublincore471914entryPoint","@type":["http:\/\/schema.org\/EntryPoint"],"http:\/\/schema.org\/url":[{"@value":"https:\/\/www.bco-dmo.org\/dataset\/471914\/dublin-core","@type":"xsd:anyURI"}],"http:\/\/schema.org\/contentType":[{"@value":"application\/xml","@type":"xsd:token"}],"http:\/\/purl.org\/dc\/terms\/conformsTo":[{"@value":"http:\/\/purl.org\/dc\/elements\/1.1\/","@type":"xsd:anyURI"}]},"_:Identifier471914":{"@id":"_:Identifier471914","@type":["http:\/\/ocean-data.org\/schema\/Identifier","http:\/\/ocean-data.org\/schema\/BCODMOIdentifier","http:\/\/ocean-data.org\/schema\/OSPREY_v2_Node_dataset"],"http:\/\/ocean-data.org\/schema\/identifierScheme":[{"@id":"http:\/\/ocean-data.org\/schema\/IdentifierScheme_BCODMO_Version_2"}],"http:\/\/ocean-data.org\/schema\/identifierValue":[{"@value":"471914","@type":"xsd:token"}],"http:\/\/ocean-data.org\/schema\/resolvableURL":[{"@value":"http:\/\/lod.bco-dmo.org\/id\/dataset\/471914","@type":"xsd:anyURI"}]}}]}