GSE27243
A Transcriptomic Atlas of Mouse Neocortical Layers
In the mammalian cortex, neurons and glia form a patterned structure across six layers whose complex cytoarchitectonic arrangement likely contributes greatly to cognitive abilities.  We sequenced transcriptomes from layers 1-6b of the adult (P56) mouse primary somatosensory cortex, along with dorsal cortex and lateral cortex, to understand the transcriptional levels and functional repertoires of coding and noncoding loci for cells that constitute these layers.  5,835 protein-coding genes and 66 noncoding RNA loci are differentially expressed (patterned) across the layers, based on 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 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 alternatively spliced transcripts that are differentially expressed across layers. Overall design: Eight adult male mice (56 days old; C57BL/6J strain) were killed by cervical dislocation according to approved schedule one UK Home Office guidelines (Scientific Procedures Act, 1986).  The eight were comprised of two groups of four littermates each.  The mice were decapitated, the skull opened down the midline and the brain removed.  Newly dissected brains were rinsed in RNAse free PBS and stored at -20°C in RNAlater (Ambion).   Whole brains were embedded in 5% agarose and sectioned using a vibrating microtome into 200 micrometer coronal sections using a 1:1 mixture of RNAlater and PBS.  Six sections corresponding approximately to cortical layers I-III, IV, upper V, lower V, VI, and VIb (henceforth referred to as samples A-F, respectively) were dissected out under visual guidance, using transillumination on a dissecting microscope (MZFLIII, Leica) and stored separately in RNAlater at -80°C until all microdissection was complete.  For RNA extraction samples from individual zones from the eight mice were combined and all tissue samples were processed at the same time.  To provide a biological replicate sample, the RNA for sample B was extracted and pooled by litter, providing two samples each representing 4 mice (heretofore known as samples B1 and B2).  In the same way, layers of dorsal cortex and lateral cortex were dissected from eight additional adult male mice.