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dc.contributor.authorValen, Eivind
dc.contributor.authorPascarella, Giovanni
dc.contributor.authorChalk, Alistair
dc.contributor.authorMaeda, Norihiro
dc.contributor.authorKojima, Miki
dc.contributor.authorKawazu, Chika
dc.contributor.authorMurata, Mitsuyoshi
dc.contributor.authorNishiyori, Hiromi
dc.contributor.authorLazarevic, Dejan
dc.contributor.authorMotti, Dario
dc.contributor.authorMarstrand, Troels Torben
dc.contributor.authorTang, Man-Hung Eric
dc.contributor.authorZhao, Xiaobei
dc.contributor.authorKrogh, Anders
dc.contributor.authorWinther, Ole
dc.contributor.authorArakawa, Takahiro
dc.contributor.authorKawai, Jun
dc.contributor.authorWells, Christine
dc.contributor.authorDaub, Carsten
dc.contributor.authorHarbers, Matthias
dc.contributor.authorHayashizaki, Yoshihide
dc.contributor.authorGustincich, Stefano
dc.contributor.authorSandelin, Albin
dc.contributor.authorCarninci, Piero
dc.contributor.editorHillary Sussman (Editor-in-Chief)
dc.date.accessioned2017-05-03T15:23:14Z
dc.date.available2017-05-03T15:23:14Z
dc.date.issued2009
dc.date.modified2010-06-29T06:44:01Z
dc.identifier.issn1088-9051
dc.identifier.doi10.1101/gr.084541.108
dc.identifier.urihttp://hdl.handle.net/10072/22543
dc.description.abstractFinding and characterizing mRNAs, their transcription start sites (TSS) and their associated promoters is a major focus in post-genome biology. Mammalian cells have at least 5-10 magnitudes more TSS than previously believed, and deeper sequencing is necessary to detect all active promoters in a given tissue. Here, we present a new method for high throughput sequencing of 5' cDNA tags, DeepCAGE: merging the Cap Analysis of Gene Expression method with ultra-high throughput sequence technology. We apply DeepCAGE to characterize 1.4 million sequenced TSS from mouse hippocampus and reveal a wealth of novel core promoters which are preferentially used in hippocampus: this is the most comprehensive promoter dataset for any tissue to date. Using this data, we present evidence indicating a key role for the Arnt2 transcription factor in hippocampus gene regulation. DeepCAGE can also detect promoters used only in a small subset of cells within the complex tissue.
dc.description.peerreviewedYes
dc.description.publicationstatusYes
dc.languageEnglish
dc.language.isoeng
dc.publisherCold Spring Harbor Laboratory Press, Publications Department
dc.publisher.placeUnited States
dc.relation.ispartofstudentpublicationN
dc.relation.ispartofpagefrom255
dc.relation.ispartofpageto265
dc.relation.ispartofissue2
dc.relation.ispartofjournalGenome Research
dc.relation.ispartofvolume19
dc.rights.retentionY
dc.subject.fieldofresearchGenomics
dc.subject.fieldofresearchBiological Sciences
dc.subject.fieldofresearchMedical and Health Sciences
dc.subject.fieldofresearchcode060408
dc.subject.fieldofresearchcode06
dc.subject.fieldofresearchcode11
dc.titleGenome-wide detection and analysis of hippocampus core promoters using DeepCAGE
dc.typeJournal article
dc.type.descriptionC1 - Articles
dc.type.codeC - Journal Articles
gro.rights.copyrightSelf-archiving of the author-manuscript version is not yet supported by this publisher. Please refer to the journal link for access to the definitive, published version or contact the authors for more information.
gro.date.issued2009
gro.hasfulltextNo Full Text
gro.griffith.authorWells, Christine
gro.griffith.authorChalk, Alistair M.


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