Ontology type: schema:ScholarlyArticle Open Access: True
2015-09
AUTHORSJohn P. Thomson, Angie Fawkes, Raffaele Ottaviano, Jennifer M. Hunter, Ruchi Shukla, Heidi K. Mjoseng, Richard Clark, Audrey Coutts, Lee Murphy, Richard R. Meehan
ABSTRACTModification of DNA resulting in 5-methylcytosine (5 mC) or 5-hydroxymethylcytosine (5hmC) has been shown to influence the local chromatin environment and affect transcription. Although recent advances in next generation sequencing technology allow researchers to map epigenetic modifications across the genome, such experiments are often time-consuming and cost prohibitive. Here we present a rapid and cost effective method of generating genome wide DNA modification maps utilising commercially available semiconductor based technology (DNA immunoprecipitation semiconductor sequencing; "DIP-SC-seq") on the Ion Proton sequencer. Focussing on the 5hmC mark we demonstrate, by directly comparing with alternative sequencing strategies, that this platform can successfully generate genome wide 5hmC patterns from as little as 500 ng of genomic DNA in less than 4 days. Such a method can therefore facilitate the rapid generation of multiple genome wide epigenetic datasets. More... »
PAGES9778
http://scigraph.springernature.com/pub.10.1038/srep09778
DOIhttp://dx.doi.org/10.1038/srep09778
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1008799336
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/25985418
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/2008/0604",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Genetics",
"type": "DefinedTerm"
},
{
"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"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Animals",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "DNA",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "DNA Methylation",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Epigenesis, Genetic",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Epigenomics",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Genome-Wide Association Study",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "High-Throughput Nucleotide Sequencing",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Immunoprecipitation",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Liver",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Mice",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "Medical Research Council Institute of Genetics and Molecular Medicine",
"id": "https://www.grid.ac/institutes/grid.415854.9",
"name": [
"MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK"
],
"type": "Organization"
},
"familyName": "Thomson",
"givenName": "John P.",
"id": "sg:person.01347530440.02",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01347530440.02"
],
"type": "Person"
},
{
"affiliation": {
"name": [
"Wellcome Trust Clinical Research Facility, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK"
],
"type": "Organization"
},
"familyName": "Fawkes",
"givenName": "Angie",
"id": "sg:person.0611134015.44",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0611134015.44"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Medical Research Council Institute of Genetics and Molecular Medicine",
"id": "https://www.grid.ac/institutes/grid.415854.9",
"name": [
"MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK"
],
"type": "Organization"
},
"familyName": "Ottaviano",
"givenName": "Raffaele",
"id": "sg:person.01365613524.41",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01365613524.41"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Medical Research Council Institute of Genetics and Molecular Medicine",
"id": "https://www.grid.ac/institutes/grid.415854.9",
"name": [
"MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK"
],
"type": "Organization"
},
"familyName": "Hunter",
"givenName": "Jennifer M.",
"id": "sg:person.0624124340.79",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0624124340.79"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Medical Research Council Institute of Genetics and Molecular Medicine",
"id": "https://www.grid.ac/institutes/grid.415854.9",
"name": [
"MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK"
],
"type": "Organization"
},
"familyName": "Shukla",
"givenName": "Ruchi",
"id": "sg:person.0773475615.30",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0773475615.30"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Medical Research Council Institute of Genetics and Molecular Medicine",
"id": "https://www.grid.ac/institutes/grid.415854.9",
"name": [
"MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK"
],
"type": "Organization"
},
"familyName": "Mjoseng",
"givenName": "Heidi K.",
"id": "sg:person.01171172476.67",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01171172476.67"
],
"type": "Person"
},
{
"affiliation": {
"name": [
"Wellcome Trust Clinical Research Facility, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK"
],
"type": "Organization"
},
"familyName": "Clark",
"givenName": "Richard",
"id": "sg:person.01107724215.70",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01107724215.70"
],
"type": "Person"
},
{
"affiliation": {
"name": [
"Wellcome Trust Clinical Research Facility, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK"
],
"type": "Organization"
},
"familyName": "Coutts",
"givenName": "Audrey",
"type": "Person"
},
{
"affiliation": {
"name": [
"Wellcome Trust Clinical Research Facility, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK"
],
"type": "Organization"
},
"familyName": "Murphy",
"givenName": "Lee",
"id": "sg:person.01336130203.67",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01336130203.67"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Medical Research Council Institute of Genetics and Molecular Medicine",
"id": "https://www.grid.ac/institutes/grid.415854.9",
"name": [
"MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK"
],
"type": "Organization"
},
"familyName": "Meehan",
"givenName": "Richard R.",
"id": "sg:person.01265211372.62",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01265211372.62"
],
"type": "Person"
}
],
"citation": [
{
"id": "https://doi.org/10.1016/j.ygeno.2014.08.017",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1001129893"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.cell.2007.05.009",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1002139821"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature08924",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1003145346",
"https://doi.org/10.1038/nature08924"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature08924",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1003145346",
"https://doi.org/10.1038/nature08924"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.cell.2012.02.045",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1005017810"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/gkt232",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1005521840"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ng1032",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1006930818",
"https://doi.org/10.1038/ng1032"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ng1032",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1006930818",
"https://doi.org/10.1038/ng1032"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature10242",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1007480955",
"https://doi.org/10.1038/nature10242"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.2217/epi.13.69",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1008422595"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/978-1-62703-706-8_20",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1010286784",
"https://doi.org/10.1007/978-1-62703-706-8_20"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/gb-2013-14-8-r91",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1013902909",
"https://doi.org/10.1186/gb-2013-14-8-r91"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.cell.2012.11.039",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1014008509"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nbt.1732",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1014644460",
"https://doi.org/10.1038/nbt.1732"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/gb-2012-13-10-r93",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1017746193",
"https://doi.org/10.1186/gb-2012-13-10-r93"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1101/gr.126417.111",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1019231884"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/bfgp/els063",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1020237064"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.5808/gi.2014.12.1.2",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1023310951"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nmeth.1684",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1023474002",
"https://doi.org/10.1038/nmeth.1684"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nprot.2012.103",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1024177835",
"https://doi.org/10.1038/nprot.2012.103"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ncb2748",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1032971592",
"https://doi.org/10.1038/ncb2748"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nbt.2398",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1036294246",
"https://doi.org/10.1038/nbt.2398"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nprot.2012.104",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1036464797",
"https://doi.org/10.1038/nprot.2012.104"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/gkt1080",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1037936759"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1038/msb.2011.95",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1038912874"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1038/msb.2011.95",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1038912874"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.mrgentox.2013.08.007",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1039422288"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/978-1-62703-706-8_19",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1041217121",
"https://doi.org/10.1007/978-1-62703-706-8_19"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.ygeno.2014.08.023",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1044414275"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/489052a",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1044958056",
"https://doi.org/10.1038/489052a"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature10008",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1045173380",
"https://doi.org/10.1038/nature10008"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.cell.2013.09.011",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1045640050"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ncomms3672",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1045991079",
"https://doi.org/10.1038/ncomms3672"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.cell.2012.04.027",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1046692465"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pone.0015367",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1050703076"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1126/science.1220671",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1052352304"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/gb-2012-13-10-2012",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1064134842",
"https://doi.org/10.1186/gb-2012-13-10-2012"
],
"type": "CreativeWork"
}
],
"datePublished": "2015-09",
"datePublishedReg": "2015-09-01",
"description": "Modification of DNA resulting in 5-methylcytosine (5 mC) or 5-hydroxymethylcytosine (5hmC) has been shown to influence the local chromatin environment and affect transcription. Although recent advances in next generation sequencing technology allow researchers to map epigenetic modifications across the genome, such experiments are often time-consuming and cost prohibitive. Here we present a rapid and cost effective method of generating genome wide DNA modification maps utilising commercially available semiconductor based technology (DNA immunoprecipitation semiconductor sequencing; \"DIP-SC-seq\") on the Ion Proton sequencer. Focussing on the 5hmC mark we demonstrate, by directly comparing with alternative sequencing strategies, that this platform can successfully generate genome wide 5hmC patterns from as little as 500 ng of genomic DNA in less than 4 days. Such a method can therefore facilitate the rapid generation of multiple genome wide epigenetic datasets.",
"genre": "research_article",
"id": "sg:pub.10.1038/srep09778",
"inLanguage": [
"en"
],
"isAccessibleForFree": true,
"isFundedItemOf": [
{
"id": "sg:grant.2780468",
"type": "MonetaryGrant"
}
],
"isPartOf": [
{
"id": "sg:journal.1045337",
"issn": [
"2045-2322"
],
"name": "Scientific Reports",
"type": "Periodical"
},
{
"issueNumber": "1",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "5"
}
],
"name": "DNA immunoprecipitation semiconductor sequencing (DIP-SC-seq) as a rapid method to\n generate genome wide epigenetic signatures",
"pagination": "9778",
"productId": [
{
"name": "readcube_id",
"type": "PropertyValue",
"value": [
"29ec92e7210d9bcf28c7c0e5ec2cd731d8d3d6ccc67ac48ffd4d9920ddcb86b2"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"25985418"
]
},
{
"name": "nlm_unique_id",
"type": "PropertyValue",
"value": [
"101563288"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1038/srep09778"
]
},
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1008799336"
]
}
],
"sameAs": [
"https://doi.org/10.1038/srep09778",
"https://app.dimensions.ai/details/publication/pub.1008799336"
],
"sdDataset": "articles",
"sdDatePublished": "2019-04-10T19:45",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8681_00000422.jsonl",
"type": "ScholarlyArticle",
"url": "http://www.nature.com/articles/srep09778"
}
]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/srep09778'
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/srep09778'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/srep09778'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/srep09778'
This table displays all metadata directly associated to this object as RDF triples.
299 TRIPLES
21 PREDICATES
73 URIs
31 LITERALS
19 BLANK NODES