{"data":{"id":"10.6084/m9.figshare.1623213","type":"dois","attributes":{"doi":"10.6084/m9.figshare.1623213","prefix":"10.6084","suffix":"m9.figshare.1623213","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Kornienko, Aleksandra E.","nameType":"Personal","givenName":"Aleksandra E.","familyName":"Kornienko","affiliation":[],"nameIdentifiers":[]},{"name":"Vlatkovic, Irena","nameType":"Personal","givenName":"Irena","familyName":"Vlatkovic","affiliation":[],"nameIdentifiers":[]},{"name":"Neesen, Jürgen","nameType":"Personal","givenName":"Jürgen","familyName":"Neesen","affiliation":[],"nameIdentifiers":[]},{"name":"Barlow, Denise P","nameType":"Personal","givenName":"Denise P","familyName":"Barlow","affiliation":[],"nameIdentifiers":[]},{"name":"Pauler, Florian M.","nameType":"Personal","givenName":"Florian M.","familyName":"Pauler","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"A human haploid gene trap collection to study lncRNAs with unusual RNA biology"}],"publisher":"Taylor \u0026 Francis","container":{},"publicationYear":2016,"subjects":[{"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":"Developmental Biology"},{"subject":"Cancer"},{"subject":"111714 Mental Health","subjectScheme":"FOR"},{"subject":"FOS: Health sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Health sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Hematology"}],"contributors":[],"dates":[{"date":"2015-12-15","dateType":"Created"},{"date":"2016-03-17","dateType":"Updated"},{"date":"2016","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsSupplementTo","relatedIdentifier":"10.1080/15476286.2015.1110676","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":["2281694 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":"Many thousand long non-coding (lnc) RNAs are mapped in the human genome. Time consuming studies using reverse genetic approaches by post-transcriptional knock-down or genetic modification of the locus demonstrated diverse biological functions for a few of these transcripts. The Human Gene Trap Mutant Collection in haploid KBM7 cells is a ready-to-use tool for studying protein-coding gene function. As lncRNAs show remarkable differences in RNA biology compared to protein-coding genes, it is unclear if this gene trap collection is useful for functional analysis of lncRNAs. Here we use the uncharacterized \u003ci\u003eLOC100288798\u003c/i\u003e lncRNA as a model to answer this question. Using public RNA-seq data we show that \u003ci\u003eLOC100288798\u003c/i\u003e is ubiquitously expressed, but inefficiently spliced. The minor spliced \u003ci\u003eLOC100288798\u003c/i\u003e isoforms are exported to the cytoplasm, whereas the major unspliced isoform is nuclear localized. This shows that \u003ci\u003eLOC100288798\u003c/i\u003e RNA biology differs markedly from typical mRNAs. \u003ci\u003eDe novo\u003c/i\u003e assembly from RNA-seq data suggests that \u003ci\u003eLOC100288798\u003c/i\u003e extends 289kb beyond its annotated 3' end and overlaps the downstream \u003ci\u003eSLC38A4\u003c/i\u003e gene. Three cell lines with independent gene trap insertions in \u003ci\u003eLOC100288798\u003c/i\u003e were available from the KBM7 gene trap collection. RT-qPCR and RNA-seq confirmed successful lncRNA truncation and its extended length. Expression analysis from RNA-seq data shows significant deregulation of 41 protein-coding genes upon \u003ci\u003eLOC100288798\u003c/i\u003e truncation. Our data shows that gene trap collections in human haploid cell lines are useful tools to study lncRNAs, and identifies the previously uncharacterized \u003ci\u003eLOC100288798\u003c/i\u003e as a potential gene regulator.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"PD94bWwgdmVyc2lvbj0iMS4wIiBlbmNvZGluZz0iVVRGLTgiPz4KPHJlc291cmNlIHhtbG5zPSJodHRwOi8vZGF0YWNpdGUub3JnL3NjaGVtYS9rZXJuZWwtNCIgeG1sbnM6eHNpPSJodHRwOi8vd3d3LnczLm9yZy8yMDAxL1hNTFNjaGVtYS1pbnN0YW5jZSIgeHNpOnNjaGVtYUxvY2F0aW9uPSJodHRwOi8vZGF0YWNpdGUub3JnL3NjaGVtYS9rZXJuZWwtNCBodHRwOi8vc2NoZW1hLmRhdGFjaXRlLm9yZy9tZXRhL2tlcm5lbC00LjEvbWV0YWRhdGEueHNkIj4KICA8aWRlbnRpZmllciBpZGVudGlmaWVyVHlwZT0iRE9JIj4xMC42MDg0L005LkZJR1NIQVJFLjE2MjMyMTM8L2lkZW50aWZpZXI+CiAgPGNyZWF0b3JzPgogICAgPGNyZWF0b3I+CiAgICAgIDxjcmVhdG9yTmFtZT5BbGVrc2FuZHJhIEUuIEtvcm5pZW5rbzwvY3JlYXRvck5hbWU+CiAgICA8L2NyZWF0b3I+CiAgICA8Y3JlYXRvcj4KICAgICAgPGNyZWF0b3JOYW1lPklyZW5hIFZsYXRrb3ZpYzwvY3JlYXRvck5hbWU+CiAgICA8L2NyZWF0b3I+CiAgICA8Y3JlYXRvcj4KICAgICAgPGNyZWF0b3JOYW1lPkrDvHJnZW4gTmVlc2VuPC9jcmVhdG9yTmFtZT4KICAgIDwvY3JlYXRvcj4KICAgIDxjcmVhdG9yPgogICAgICA8Y3JlYXRvck5hbWU+RGVuaXNlIFAgQmFybG93PC9jcmVhdG9yTmFtZT4KICAgIDwvY3JlYXRvcj4KICAgIDxjcmVhdG9yPgogICAgICA8Y3JlYXRvck5hbWU+RmxvcmlhbiBNLiBQYXVsZXI8L2NyZWF0b3JOYW1lPgogICAgPC9jcmVhdG9yPgogIDwvY3JlYXRvcnM+CiAgPHRpdGxlcz4KICAgIDx0aXRsZT5BIGh1bWFuIGhhcGxvaWQgZ2VuZSB0cmFwIGNvbGxlY3Rpb24gdG8gc3R1ZHkgbG5jUk5BcyB3aXRoIHVudXN1YWwgUk5BIGJpb2xvZ3k8L3RpdGxlPgogIDwvdGl0bGVzPgogIDxkZXNjcmlwdGlvbnM+CiAgICA8ZGVzY3JpcHRpb24gZGVzY3JpcHRpb25UeXBlPSJBYnN0cmFjdCI+Jmx0O3AmZ3Q7TWFueSB0aG91c2FuZCBsb25nIG5vbi1jb2RpbmcgKGxuYykgUk5BcyBhcmUgbWFwcGVkIGluIHRoZSBodW1hbiBnZW5vbWUuIFRpbWUgY29uc3VtaW5nIHN0dWRpZXMgdXNpbmcgcmV2ZXJzZSBnZW5ldGljIGFwcHJvYWNoZXMgYnkgcG9zdC10cmFuc2NyaXB0aW9uYWwga25vY2stZG93biBvciBnZW5ldGljIG1vZGlmaWNhdGlvbiBvZiB0aGUgbG9jdXMgZGVtb25zdHJhdGVkIGRpdmVyc2UgYmlvbG9naWNhbCBmdW5jdGlvbnMgZm9yIGEgZmV3IG9mIHRoZXNlIHRyYW5zY3JpcHRzLiBUaGUgSHVtYW4gR2VuZSBUcmFwIE11dGFudCBDb2xsZWN0aW9uIGluIGhhcGxvaWQgS0JNNyBjZWxscyBpcyBhIHJlYWR5LXRvLXVzZSB0b29sIGZvciBzdHVkeWluZyBwcm90ZWluLWNvZGluZyBnZW5lIGZ1bmN0aW9uLiBBcyBsbmNSTkFzIHNob3cgcmVtYXJrYWJsZSBkaWZmZXJlbmNlcyBpbiBSTkEgYmlvbG9neSBjb21wYXJlZCB0byBwcm90ZWluLWNvZGluZyBnZW5lcywgaXQgaXMgdW5jbGVhciBpZiB0aGlzIGdlbmUgdHJhcCBjb2xsZWN0aW9uIGlzIHVzZWZ1bCBmb3IgZnVuY3Rpb25hbCBhbmFseXNpcyBvZiBsbmNSTkFzLiBIZXJlIHdlIHVzZSB0aGUgdW5jaGFyYWN0ZXJpemVkICZsdDtpJmd0O0xPQzEwMDI4ODc5OCZsdDsvaSZndDsgbG5jUk5BIGFzIGEgbW9kZWwgdG8gYW5zd2VyIHRoaXMgcXVlc3Rpb24uIFVzaW5nIHB1YmxpYyBSTkEtc2VxIGRhdGEgd2Ugc2hvdyB0aGF0ICZsdDtpJmd0O0xPQzEwMDI4ODc5OCZsdDsvaSZndDsgaXMgdWJpcXVpdG91c2x5IGV4cHJlc3NlZCwgYnV0IGluZWZmaWNpZW50bHkgc3BsaWNlZC4gVGhlIG1pbm9yIHNwbGljZWQgJmx0O2kmZ3Q7TE9DMTAwMjg4Nzk4Jmx0Oy9pJmd0OyBpc29mb3JtcyBhcmUgZXhwb3J0ZWQgdG8gdGhlIGN5dG9wbGFzbSwgd2hlcmVhcyB0aGUgbWFqb3IgdW5zcGxpY2VkIGlzb2Zvcm0gaXMgbnVjbGVhciBsb2NhbGl6ZWQuIFRoaXMgc2hvd3MgdGhhdCAmbHQ7aSZndDtMT0MxMDAyODg3OTgmbHQ7L2kmZ3Q7IFJOQSBiaW9sb2d5IGRpZmZlcnMgbWFya2VkbHkgZnJvbSB0eXBpY2FsIG1STkFzLiAmbHQ7aSZndDtEZSBub3ZvJmx0Oy9pJmd0OyBhc3NlbWJseSBmcm9tIFJOQS1zZXEgZGF0YSBzdWdnZXN0cyB0aGF0ICZsdDtpJmd0O0xPQzEwMDI4ODc5OCZsdDsvaSZndDsgZXh0ZW5kcyAyODlrYiBiZXlvbmQgaXRzIGFubm90YXRlZCAzJyBlbmQgYW5kIG92ZXJsYXBzIHRoZSBkb3duc3RyZWFtICZsdDtpJmd0O1NMQzM4QTQmbHQ7L2kmZ3Q7IGdlbmUuIFRocmVlIGNlbGwgbGluZXMgd2l0aCBpbmRlcGVuZGVudCBnZW5lIHRyYXAgaW5zZXJ0aW9ucyBpbiAmbHQ7aSZndDtMT0MxMDAyODg3OTgmbHQ7L2kmZ3Q7IHdlcmUgYXZhaWxhYmxlIGZyb20gdGhlIEtCTTcgZ2VuZSB0cmFwIGNvbGxlY3Rpb24uIFJULXFQQ1IgYW5kIFJOQS1zZXEgY29uZmlybWVkIHN1Y2Nlc3NmdWwgbG5jUk5BIHRydW5jYXRpb24gYW5kIGl0cyBleHRlbmRlZCBsZW5ndGguIEV4cHJlc3Npb24gYW5hbHlzaXMgZnJvbSBSTkEtc2VxIGRhdGEgc2hvd3Mgc2lnbmlmaWNhbnQgZGVyZWd1bGF0aW9uIG9mIDQxIHByb3RlaW4tY29kaW5nIGdlbmVzIHVwb24gJmx0O2kmZ3Q7TE9DMTAwMjg4Nzk4Jmx0Oy9pJmd0OyB0cnVuY2F0aW9uLiBPdXIgZGF0YSBzaG93cyB0aGF0IGdlbmUgdHJhcCBjb2xsZWN0aW9ucyBpbiBodW1hbiBoYXBsb2lkIGNlbGwgbGluZXMgYXJlIHVzZWZ1bCB0b29scyB0byBzdHVkeSBsbmNSTkFzLCBhbmQgaWRlbnRpZmllcyB0aGUgcHJldmlvdXNseSB1bmNoYXJhY3Rlcml6ZWQgJmx0O2kmZ3Q7TE9DMTAwMjg4Nzk4Jmx0Oy9pJmd0OyBhcyBhIHBvdGVudGlhbCBnZW5lIHJlZ3VsYXRvci4mbHQ7L3AmZ3Q7PC9kZXNjcmlwdGlvbj4KICA8L2Rlc2NyaXB0aW9ucz4KICA8c3ViamVjdHM+CiAgICA8c3ViamVjdD5DZWxsIEJpb2xvZ3k8L3N1YmplY3Q+CiAgICA8c3ViamVjdD5HZW5ldGljczwvc3ViamVjdD4KICAgIDxzdWJqZWN0Pk1vbGVjdWxhciBCaW9sb2d5PC9zdWJqZWN0PgogICAgPHN1YmplY3Qgc2NoZW1lVVJJPSJodHRwOi8vd3d3LmFicy5nb3YuYXUvYXVzc3RhdHMvYWJzQC5uc2YvMC82QkI0MjdBQjk2OTZDMjI1Q0EyNTc0MTgwMDA0NDYzRSIgc3ViamVjdFNjaGVtZT0iRk9SIj41OTk5OSBFbnZpcm9ubWVudGFsIFNjaWVuY2VzIG5vdCBlbHNld2hlcmUgY2xhc3NpZmllZDwvc3ViamVjdD4KICAgIDxzdWJqZWN0IHNjaGVtZVVSST0iaHR0cDovL3d3dy5hYnMuZ292LmF1L2F1c3N0YXRzL2Fic0AubnNmLzAvNkJCNDI3QUI5Njk2QzIyNUNBMjU3NDE4MDAwNDQ2M0UiIHN1YmplY3RTY2hlbWU9IkZPUiI+Njk5OTkgQmlvbG9naWNhbCBTY2llbmNlcyBub3QgZWxzZXdoZXJlIGNsYXNzaWZpZWQ8L3N1YmplY3Q+CiAgICA8c3ViamVjdD5EZXZlbG9wbWVudGFsIEJpb2xvZ3k8L3N1YmplY3Q+CiAgICA8c3ViamVjdD5DYW5jZXI8L3N1YmplY3Q+CiAgICA8c3ViamVjdCBzY2hlbWVVUkk9Imh0dHA6Ly93d3cuYWJzLmdvdi5hdS9hdXNzdGF0cy9hYnNALm5zZi8wLzZCQjQyN0FCOTY5NkMyMjVDQTI1NzQxODAwMDQ0NjNFIiBzdWJqZWN0U2NoZW1lPSJGT1IiPjExMTcxNCBNZW50YWwgSGVhbHRoPC9zdWJqZWN0PgogICAgPHN1YmplY3Q+SGVtYXRvbG9neTwvc3ViamVjdD4KICA8L3N1YmplY3RzPgogIDxwdWJsaXNoZXI+VGF5bG9yICZhbXA7IEZyYW5jaXM8L3B1Ymxpc2hlcj4KICA8cHVibGljYXRpb25ZZWFyPjIwMTY8L3B1YmxpY2F0aW9uW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