Ontology type: schema:ScholarlyArticle Open Access: True
2016-12-20
AUTHORSChristophe J. Langouet-Astrie, Annamarie L. Meinsen, Emily R. Grunwald, Stephen D. Turner, Raymond A. Enke
ABSTRACTRNA sequencing transcriptome analysis using massively parallel next generation sequencing technology provides the capability to understand global changes in gene expression throughout a range of tissue samples. Development of the vertebrate retina requires complex temporal orchestration of transcriptional activation and repression. The chicken embryo (Gallus gallus) is a classic model system for studying developmental biology and retinogenesis. Existing retinal transcriptome projects have been critical to the vision research community for studying aspects of murine and human retinogenesis, however, there are currently no publicly available data sets describing the developing chicken retinal transcriptome. Here we used Illumina RNA sequencing (RNA-seq) analysis to characterize the mRNA transcriptome of the developing chicken retina in an effort to identify genes critical for retinal development in this important model organism. These data will be valuable to the vision research community for characterizing global changes in gene expression between ocular tissues and critical developmental time points during retinogenesis in the chicken retina. More... »
PAGES160117
http://scigraph.springernature.com/pub.10.1038/sdata.2016.117
DOIhttp://dx.doi.org/10.1038/sdata.2016.117
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1017713388
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/27996968
JSON-LD is the canonical representation for SciGraph data.
TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT
[
{
"@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json",
"about": [
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Biological Sciences",
"type": "DefinedTerm"
},
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Genetics",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Animals",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Chick Embryo",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "RNA, Messenger",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Retina",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Sequence Analysis, RNA",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Transcriptome",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "Department of Biology, James Madison University, 22807, Harrisonburg, Virginia, USA",
"id": "http://www.grid.ac/institutes/grid.258041.a",
"name": [
"Department of Biology, James Madison University, 22807, Harrisonburg, Virginia, USA"
],
"type": "Organization"
},
"familyName": "Langouet-Astrie",
"givenName": "Christophe J.",
"id": "sg:person.014263430655.16",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014263430655.16"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Biology, James Madison University, 22807, Harrisonburg, Virginia, USA",
"id": "http://www.grid.ac/institutes/grid.258041.a",
"name": [
"Department of Biology, James Madison University, 22807, Harrisonburg, Virginia, USA"
],
"type": "Organization"
},
"familyName": "Meinsen",
"givenName": "Annamarie L.",
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Biology, James Madison University, 22807, Harrisonburg, Virginia, USA",
"id": "http://www.grid.ac/institutes/grid.258041.a",
"name": [
"Department of Biology, James Madison University, 22807, Harrisonburg, Virginia, USA"
],
"type": "Organization"
},
"familyName": "Grunwald",
"givenName": "Emily R.",
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Public Health Sciences University of Virginia, 22908, Charlottesville, Virginia, USA",
"id": "http://www.grid.ac/institutes/grid.27755.32",
"name": [
"Department of Public Health Sciences University of Virginia, 22908, Charlottesville, Virginia, USA"
],
"type": "Organization"
},
"familyName": "Turner",
"givenName": "Stephen D.",
"id": "sg:person.01327125007.27",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01327125007.27"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Center for Genome & Metagenome Studies, James Madison University, 22807, Harrisonburg, Virginia, USA",
"id": "http://www.grid.ac/institutes/grid.258041.a",
"name": [
"Department of Biology, James Madison University, 22807, Harrisonburg, Virginia, USA",
"Center for Genome & Metagenome Studies, James Madison University, 22807, Harrisonburg, Virginia, USA"
],
"type": "Organization"
},
"familyName": "Enke",
"givenName": "Raymond A.",
"id": "sg:person.01035511146.16",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01035511146.16"
],
"type": "Person"
}
],
"citation": [
{
"id": "sg:pub.10.1038/nprot.2016.095",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1004211338",
"https://doi.org/10.1038/nprot.2016.095"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nbt.1754",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1019307928",
"https://doi.org/10.1038/nbt.1754"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/gb-2010-11-10-r106",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1031289083",
"https://doi.org/10.1186/gb-2010-11-10-r106"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/1471-213x-10-8",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1000769901",
"https://doi.org/10.1186/1471-213x-10-8"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/1749-8104-7-22",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1041852928",
"https://doi.org/10.1186/1749-8104-7-22"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nbt.2862",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1011219673",
"https://doi.org/10.1038/nbt.2862"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nrn2283",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1040607897",
"https://doi.org/10.1038/nrn2283"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s13059-014-0550-8",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1015222646",
"https://doi.org/10.1186/s13059-014-0550-8"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s13059-016-0881-8",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1041902478",
"https://doi.org/10.1186/s13059-016-0881-8"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nbt.3519",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1024493480",
"https://doi.org/10.1038/nbt.3519"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nbt.2450",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1045152751",
"https://doi.org/10.1038/nbt.2450"
],
"type": "CreativeWork"
}
],
"datePublished": "2016-12-20",
"datePublishedReg": "2016-12-20",
"description": "RNA sequencing transcriptome analysis using massively parallel next generation sequencing technology provides the capability to understand global changes in gene expression throughout a range of tissue samples. Development of the vertebrate retina requires complex temporal orchestration of transcriptional activation and repression. The chicken embryo (Gallus gallus) is a classic model system for studying developmental biology and retinogenesis. Existing retinal transcriptome projects have been critical to the vision research community for studying aspects of murine and human retinogenesis, however, there are currently no publicly available data sets describing the developing chicken retinal transcriptome. Here we used Illumina RNA sequencing (RNA-seq) analysis to characterize the mRNA transcriptome of the developing chicken retina in an effort to identify genes critical for retinal development in this important model organism. These data will be valuable to the vision research community for characterizing global changes in gene expression between ocular tissues and critical developmental time points during retinogenesis in the chicken retina.",
"genre": "article",
"id": "sg:pub.10.1038/sdata.2016.117",
"inLanguage": "en",
"isAccessibleForFree": true,
"isFundedItemOf": [
{
"id": "sg:grant.3005398",
"type": "MonetaryGrant"
}
],
"isPartOf": [
{
"id": "sg:journal.1050678",
"issn": [
"2052-4463"
],
"name": "Scientific Data",
"publisher": "Springer Nature",
"type": "Periodical"
},
{
"issueNumber": "1",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "3"
}
],
"keywords": [
"RNA sequencing analysis",
"parallel next-generation sequencing technologies",
"gene expression",
"important model organism",
"sequencing analysis",
"global change",
"classic model system",
"next-generation sequencing technologies",
"generation sequencing technology",
"critical developmental time points",
"developmental time points",
"model organisms",
"transcriptome projects",
"transcriptome analysis",
"developmental biology",
"transcriptional activation",
"mRNA transcriptome",
"temporal orchestration",
"sequencing technologies",
"retinal transcriptome",
"chicken retina",
"retinal development",
"retinogenesis",
"transcriptome",
"vertebrate retina",
"chicken embryos",
"model system",
"human retinogenesis",
"expression",
"repression",
"genes",
"RNA",
"organisms",
"biology",
"embryos",
"tissue samples",
"murine",
"community",
"activation",
"research community",
"retina",
"tissue",
"available data sets",
"development",
"analysis",
"orchestration",
"changes",
"time points",
"data sets",
"ocular tissues",
"vision research community",
"efforts",
"aspects",
"range",
"data",
"set",
"samples",
"system",
"technology",
"capability",
"point",
"project"
],
"name": "RNA sequencing analysis of the developing chicken retina",
"pagination": "160117",
"productId": [
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1017713388"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1038/sdata.2016.117"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"27996968"
]
}
],
"sameAs": [
"https://doi.org/10.1038/sdata.2016.117",
"https://app.dimensions.ai/details/publication/pub.1017713388"
],
"sdDataset": "articles",
"sdDatePublished": "2022-05-10T10:17",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-springernature-scigraph/baseset/20220509/entities/gbq_results/article/article_716.jsonl",
"type": "ScholarlyArticle",
"url": "https://doi.org/10.1038/sdata.2016.117"
}
]Download the RDF metadata as: json-ld nt turtle xml License info
JSON-LD is a popular format for linked data which is fully compatible with JSON.
curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/sdata.2016.117'
N-Triples is a line-based linked data format ideal for batch operations.
curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/sdata.2016.117'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/sdata.2016.117'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/sdata.2016.117'
This table displays all metadata directly associated to this object as RDF triples.
224 TRIPLES
22 PREDICATES
105 URIs
86 LITERALS
13 BLANK NODES