{"data":{"id":"10.6084/m9.figshare.1304578","type":"dois","attributes":{"doi":"10.6084/m9.figshare.1304578","prefix":"10.6084","suffix":"m9.figshare.1304578","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Fort, Alexandre","nameType":"Personal","givenName":"Alexandre","familyName":"Fort","affiliation":[],"nameIdentifiers":[]},{"name":"Yamada, Daisuke","nameType":"Personal","givenName":"Daisuke","familyName":"Yamada","affiliation":[],"nameIdentifiers":[]},{"name":"Hashimoto, Kosuke","nameType":"Personal","givenName":"Kosuke","familyName":"Hashimoto","affiliation":[],"nameIdentifiers":[]},{"name":"Koseki, Haruhiko","nameType":"Personal","givenName":"Haruhiko","familyName":"Koseki","affiliation":[],"nameIdentifiers":[]},{"name":"Carninci, Piero","nameType":"Personal","givenName":"Piero","familyName":"Carninci","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Nuclear transcriptome profiling of induced pluripotent stem cells and embryonic stem cells identify non-coding loci resistant to reprogramming"}],"publisher":"Taylor \u0026 Francis","container":{},"publicationYear":2015,"subjects":[{"subject":"Medicine"},{"subject":"Cell Biology"},{"subject":"Genetics"},{"subject":"FOS: Biological sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Biological sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Molecular Biology"},{"subject":"59999 Environmental Sciences not elsewhere classified","subjectScheme":"FOR"},{"subject":"FOS: Earth and related environmental sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Earth and related environmental sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"69999 Biological Sciences not elsewhere classified","subjectScheme":"FOR"},{"subject":"80699 Information Systems not elsewhere classified","subjectScheme":"FOR"},{"subject":"FOS: Computer and information sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Computer and information sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Developmental Biology"},{"subject":"Cancer"}],"contributors":[],"dates":[{"date":"2015-02-09","dateType":"Created"},{"date":"2019-04-02","dateType":"Updated"},{"date":"2015","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsSupplementTo","relatedIdentifier":"10.4161/15384101.2014.988031","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":["5187505 Bytes"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"Identification of functionally relevant differences between induced pluripotent stem cells (iPSC) and reference embryonic stem cells (ESC) remains a central question for therapeutic applications. Differences in gene expression between iPSC and ESC have been examined by microarray and more recently with RNA-SEQ technologies. We here report an in depth analyses of nuclear and cytoplasmic transcriptomes, using the CAGE (cap analysis of gene expression) technology, for 5 iPSC clones derived from mouse lymphocytes B and 3 ESC lines. This approach reveals nuclear transcriptomes significantly more complex in ESC than in iPSC. Hundreds of yet not annotated putative non-coding RNAs and enhancer-associated transcripts specifically transcribed in ESC have been detected and supported with epigenetic and chromatin-chromatin interactions data. We identified super-enhancers transcriptionally active specifically in ESC and associated with genes implicated in the maintenance of pluripotency. Similarly, we detected non-coding transcripts of yet unknown function being regulated by ESC specific super-enhancers. Taken together, these results demonstrate that current protocols of iPSC reprogramming do not trigger activation of numerous \u003ci\u003ecis\u003c/i\u003e-regulatory regions. It thus reinforces the need for already suggested deeper monitoring of the non-coding transcriptome when characterizing iPSC clones. Such differences in regulatory transcript expression may indeed impact their potential for clinical applications.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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