title: A transcriptomic atlas of mouse neocortical layers.
abstract: In the mammalian cortex, neurons and glia form a patterned structure across six layers whose complex cytoarchitectonic arrangement is likely to contribute to cognition. We sequenced transcriptomes from layers 1-6b of different areas (primary and secondary) of the adult (postnatal day 56) mouse somatosensory cortex to understand the transcriptional levels and functional repertoires of coding and noncoding loci for cells constituting these layers. A total of 5,835 protein-coding genes and 66 noncoding RNA loci are differentially expressed ("patterned") across the layers, on the basis of a machine-learning model (naive Bayes) approach. Layers 2-6b are each associated with specific functional and disease annotations that provide insights into their biological roles. This new resource (http://genserv.anat.ox.ac.uk/layers) greatly extends currently available resources, such as the Allen Mouse Brain Atlas and microarray data sets, by providing quantitative expression levels, by being genome-wide, by including novel loci, and by identifying candidate alternatively spliced transcripts that are differentially expressed across layers.
authors.affiliation: MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK.
authors.forename: T Grant
authors.initials: TG
authors.lastname: Belgard
authors.forename: Ana C
authors.initials: AC
authors.lastname: Marques
authors.forename: Peter L
authors.initials: PL
authors.lastname: Oliver
authors.forename: Hatice Ozel
authors.initials: HO
authors.lastname: Abaan
authors.forename: Tamara M
authors.initials: TM
authors.lastname: Sirey
authors.forename: Anna
authors.initials: A
authors.lastname: Hoerder-Suabedissen
authors.forename: Fernando
authors.initials: F
authors.lastname: García-Moreno
authors.forename: Zoltán
authors.initials: Z
authors.lastname: Molnár
authors.forename: Elliott H
authors.initials: EH
authors.lastname: Margulies
authors.forename: Chris P
authors.initials: CP
authors.lastname: Ponting
mesh_terms: D000716:Anatomy, Artistic; D000818:Animals; D001271:Atlases as Topic; D001499:Bayes Theorem; D015870:Gene Expression; D020869:Gene Expression Profiling; D051379:Mice; D046228:Microarray Analysis; D012313:RNA / Q000378:metabolism; D022661:RNA, Untranslated / Q000378:metabolism; D013003:Somatosensory Cortex / Q000033:anatomy & histology* / Q000737:chemistry*
chemical_list: D022661:RNA, Untranslated; D012313:RNA