{"id":"https://openalex.org/W3004267045","doi":"https://doi.org/10.1038/s41597-020-0372-3","title":"RNA proximity sequencing data and analysis pipeline from a human neuroblastoma nuclear transcriptome","display_name":"RNA proximity sequencing data and analysis pipeline from a human neuroblastoma nuclear transcriptome","publication_year":2020,"publication_date":"2020-01-28","ids":{"openalex":"https://openalex.org/W3004267045","doi":"https://doi.org/10.1038/s41597-020-0372-3","mag":"3004267045","pmid":"https://pubmed.ncbi.nlm.nih.gov/31992717","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/6987088"},"language":"en","primary_location":{"id":"doi:10.1038/s41597-020-0372-3","doi":"https://doi.org/10.1038/s41597-020-0372-3","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s41597-020-0372-3","pdf_url":"https://www.nature.com/articles/s41597-020-0372-3.pdf","source":{"id":"https://openalex.org/S2607323502","display_name":"Scientific Data","issn_l":"2052-4463","issn":["2052-4463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-b","jufo-1","ki-jl-1","medline","norway-2","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Scientific Data","raw_type":"journal-article"},"volume":null,"type":"data-paper","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.nature.com/articles/s41597-020-0372-3.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021800276","display_name":"Steven Wingett","orcid":"https://orcid.org/0000-0002-2343-0711","observed_orcids":["https://orcid.org/0000-0002-2343-0711"]},"institutions":[{"id":"https://openalex.org/I1302113299","display_name":"Babraham Institute","ror":"https://ror.org/01d5qpn59","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1302113299","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Steven W. Wingett","raw_affiliation_strings":["Bioinformatics, Babraham Institute, Cambridge, UK. steven.wingett@babraham.ac.uk","Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, UK. steven.wingett@babraham.ac.uk","Bioinformatics, Babraham Institute, Cambridge, UK"],"raw_orcid":"https://orcid.org/0000-0002-2343-0711","affiliations":[{"raw_affiliation_string":"Bioinformatics, Babraham Institute, Cambridge, UK. steven.wingett@babraham.ac.uk","institution_ids":["https://openalex.org/I1302113299"]},{"raw_affiliation_string":"Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, UK. steven.wingett@babraham.ac.uk","institution_ids":["https://openalex.org/I1302113299"]},{"raw_affiliation_string":"Bioinformatics, Babraham Institute, Cambridge, UK","institution_ids":["https://openalex.org/I1302113299"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007222510","display_name":"Simon Andrews","orcid":"https://orcid.org/0000-0002-5006-3507","observed_orcids":["https://orcid.org/0000-0002-5006-3507"]},"institutions":[{"id":"https://openalex.org/I1302113299","display_name":"Babraham Institute","ror":"https://ror.org/01d5qpn59","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1302113299","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Simon Andrews","raw_affiliation_strings":["Bioinformatics, Babraham Institute, Cambridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics, Babraham Institute, Cambridge, UK","institution_ids":["https://openalex.org/I1302113299"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049273208","display_name":"Peter Fraser","orcid":"https://orcid.org/0000-0002-0041-1227","observed_orcids":["https://orcid.org/0000-0002-0041-1227"]},"institutions":[{"id":"https://openalex.org/I103163165","display_name":"Florida State University","ror":"https://ror.org/05g3dte14","country_code":"US","type":"education","lineage":["https://openalex.org/I103163165"]},{"id":"https://openalex.org/I1302113299","display_name":"Babraham Institute","ror":"https://ror.org/01d5qpn59","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1302113299","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB","US"],"is_corresponding":false,"raw_author_name":"Peter Fraser","raw_affiliation_strings":["Department of Biological Science, Florida State University, Tallahassee, FL, USA","Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, UK","Department of Biological Science, Florida State University, Tallahassee, USA"],"raw_orcid":"https://orcid.org/0000-0002-0041-1227","affiliations":[{"raw_affiliation_string":"Department of Biological Science, Florida State University, Tallahassee, FL, USA","institution_ids":["https://openalex.org/I103163165"]},{"raw_affiliation_string":"Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, UK","institution_ids":["https://openalex.org/I1302113299"]},{"raw_affiliation_string":"Department of Biological Science, Florida State University, Tallahassee, USA","institution_ids":["https://openalex.org/I103163165"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063127241","display_name":"J\u00f6rg Morf","orcid":"https://orcid.org/0000-0002-0485-3380","observed_orcids":["https://orcid.org/0000-0002-0485-3380"]},"institutions":[{"id":"https://openalex.org/I1302113299","display_name":"Babraham Institute","ror":"https://ror.org/01d5qpn59","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1302113299","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"J\u00f6rg Morf","raw_affiliation_strings":["Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, UK. jorg.morf@gmail.com","Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, UK"],"raw_orcid":"https://orcid.org/0000-0002-0485-3380","affiliations":[{"raw_affiliation_string":"Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, UK. jorg.morf@gmail.com","institution_ids":["https://openalex.org/I1302113299"]},{"raw_affiliation_string":"Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, UK","institution_ids":["https://openalex.org/I1302113299"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5021800276","https://openalex.org/A5063127241"],"corresponding_institution_ids":["https://openalex.org/I1302113299"],"apc_list":{"value":1870,"currency":"USD","value_usd":1870},"apc_paid":{"value":1870,"currency":"USD","value_usd":1870},"fwci":null,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"7","issue":"1","first_page":"35","last_page":"35"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13127","display_name":"Biotin and Related Studies","score":0.3562000095844269,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T13127","display_name":"Biotin and Related Studies","score":0.3562000095844269,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.24210000038146973,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.15299999713897705,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/neuroblastoma","display_name":"neuroblastoma","score":0.7900000214576721},{"id":"https://openalex.org/keywords/sh-sy5y-cells","display_name":"SH-SY5Y cells","score":0.9879999756813049},{"id":"https://openalex.org/keywords/nuclear-transcriptome","display_name":"nuclear transcriptome","score":0.9409999847412109},{"id":"https://openalex.org/keywords/monte-carlo-simulation","display_name":"Monte Carlo simulation","score":0.7570000290870667},{"id":"https://openalex.org/keywords/transcript-annotation","display_name":"transcript annotation","score":0.5910000205039978}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6818360090255737},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6360741257667542},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6297463178634644},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.6101377010345459},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5532132387161255},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.48706844449043274},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45002418756484985},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.44438275694847107},{"id":"https://openalex.org/C142575336","wikidata":"https://www.wikidata.org/wiki/Q412148","display_name":"Polyadenylation","level":4,"score":0.4314482808113098},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27617090940475464},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2704836130142212},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2636331021785736},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009447","descriptor_name":"Neuroblastoma","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D018076","descriptor_name":"DNA, Complementary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058893","descriptor_name":"DNA Barcoding, Taxonomic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1038/s41597-020-0372-3","doi":"https://doi.org/10.1038/s41597-020-0372-3","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s41597-020-0372-3","pdf_url":"https://www.nature.com/articles/s41597-020-0372-3.pdf","source":{"id":"https://openalex.org/S2607323502","display_name":"Scientific Data","issn_l":"2052-4463","issn":["2052-4463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-b","jufo-1","ki-jl-1","medline","norway-2","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Scientific Data","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6987088","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6987088","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Sci Data","raw_type":"Text"},{"id":"pmid:31992717","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31992717","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Scientific data","raw_type":"Dataset"},{"id":"pmh:oai:doaj.org/article:39be0a3607c74439b6b0dc563c2f9345","doi":null,"is_oa":false,"landing_page_url":"https://doaj.org/article/39be0a3607c74439b6b0dc563c2f9345","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Scientific Data, Vol 7, Iss 1, Pp 1-14 (2020)","raw_type":"article"},{"id":"pmh:oai:www.repository.cam.ac.uk:1810/303900","doi":null,"is_oa":true,"landing_page_url":"https://www.repository.cam.ac.uk/handle/1810/303900","pdf_url":null,"source":{"id":"https://openalex.org/S4306401777","display_name":"Apollo (University of Cambridge)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I241749","host_organization_name":"University of Cambridge","host_organization_lineage":["https://openalex.org/I241749"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"doi:10.17863/cam.50984","doi":"https://doi.org/10.17863/cam.50984","is_oa":true,"landing_page_url":"https://doi.org/10.17863/cam.50984","pdf_url":null,"source":{"id":"https://openalex.org/S7407050737","display_name":"Apollo","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"JournalArticle"}],"best_oa_location":{"id":"doi:10.1038/s41597-020-0372-3","doi":"https://doi.org/10.1038/s41597-020-0372-3","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s41597-020-0372-3","pdf_url":"https://www.nature.com/articles/s41597-020-0372-3.pdf","source":{"id":"https://openalex.org/S2607323502","display_name":"Scientific Data","issn_l":"2052-4463","issn":["2052-4463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-b","jufo-1","ki-jl-1","medline","norway-2","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Scientific Data","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3004267045.pdf","grobid_xml":"https://content.openalex.org/works/W3004267045.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1535005173","https://openalex.org/W1970397315","https://openalex.org/W1985717866","https://openalex.org/W2036853573","https://openalex.org/W2067342057","https://openalex.org/W2090037139","https://openalex.org/W2102278945","https://openalex.org/W2152605077","https://openalex.org/W2159675211","https://openalex.org/W2168710870","https://openalex.org/W2170551349","https://openalex.org/W2540331622","https://openalex.org/W2594322138","https://openalex.org/W2898279863","https://openalex.org/W2910274521","https://openalex.org/W2927886090","https://openalex.org/W2955660290","https://openalex.org/W3085653884","https://openalex.org/W4240924657","https://openalex.org/W4246488417"],"related_works":["https://openalex.org/W3042832713","https://openalex.org/W2955660290","https://openalex.org/W2760956924","https://openalex.org/W2971191817","https://openalex.org/W4367836905","https://openalex.org/W7160833455","https://openalex.org/W3202391795","https://openalex.org/W2905302482","https://openalex.org/W7161264623","https://openalex.org/W3211552895"],"abstract_inverted_index":{"We":[0,116],"have":[1],"previously":[2],"developed":[3],"and":[4,25,51,65,127,134,152],"described":[5],"a":[6,61,137],"method":[7],"for":[8,99,107,112,155],"measuring":[9],"RNA":[10,21,108],"co-locations":[11],"within":[12],"cells,":[13],"called":[14],"Proximity":[15],"RNA-seq,":[16],"which":[17,57,86],"promises":[18],"insights":[19],"into":[20],"expression,":[22],"processing,":[23],"storage":[24],"translation.":[26],"Here,":[27],"we":[28,48],"describe":[29,50],"transcriptome-wide":[30],"proximity":[31],"RNA-seq":[32],"datasets":[33,126],"obtained":[34],"from":[35],"human":[36],"neuroblastoma":[37],"SH-SY5Y":[38],"cell":[39],"nuclei.":[40],"To":[41],"aid":[42],"future":[43],"users":[44],"of":[45,84,150],"this":[46,119],"method,":[47],"also":[49],"release":[52],"our":[53],"analysis":[54],"pipeline,":[55],"CloseCall,":[56],"maps":[58],"cDNA":[59],"to":[60,69,81,123,136],"custom":[62],"transcript":[63],"annotation":[64],"allocates":[66],"cDNA-linked":[67],"barcodes":[68],"barcode":[70],"groups.":[71],"CloseCall":[72],"then":[73],"performs":[74],"Monte":[75],"Carlo":[76],"simulations":[77],"on":[78],"the":[79,130,147],"data":[80,132,145],"identify":[82],"pairs":[83],"transcripts,":[85,101],"are":[87],"co-barcoded":[88],"more":[89],"frequently":[90],"than":[91],"expected":[92],"by":[93],"chance.":[94],"Furthermore,":[95],"derived":[96],"co-barcoding":[97],"frequencies":[98],"individual":[100],"dubbed":[102],"valency,":[103],"serve":[104],"as":[105],"proxies":[106],"density":[109],"or":[110],"connectivity":[111],"that":[113,140],"given":[114],"transcript.":[115],"outline":[117],"how":[118],"pipeline":[120],"was":[121],"applied":[122],"these":[124],"sequencing":[125],"openly":[128],"share":[129],"processed":[131],"outputs":[133],"access":[135],"virtual":[138],"machine":[139],"runs":[141],"CloseCall.":[142],"The":[143],"resulting":[144],"specify":[146],"spatial":[148],"organization":[149],"RNAs":[151],"builds":[153],"hypotheses":[154],"potential":[156],"regulatory":[157],"relationships":[158],"between":[159],"RNAs.":[160]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":3}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2020-02-07T00:00:00"}
