A Transcriptomic Atlas of Mouse Neocortical Layers

Abstract

SummaryIn 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.

Improved definition of the mouse transcriptome via targeted RNA sequencing

“…Mouse lncRNAs were identified by updating and extending the method outlined in Clark et al (2012). Mouse RNAs were obtained from the following sources: the UCSC mm9 mRNA track (alignments between GenBank RNAs and the genome), UCSC genes (predictions based on RefSeq, GenBank, and the tRNA Genes track) (Kent et al 2002), and RefSeq genes (Pruitt et al 2012) (downloaded April 10, 2012); also included were lincRNAs identified in Belgard et al (2011), transcripts overlapping novel lincRNA loci identified in Guttman et al (2010), and transcripts overlapping lincRNA loci investigated by Guttman et al (2011).…”

From sauropsids to mammals and back: New approaches to comparative cortical development

“…In the human cortex we observed that subplate subpopulations show increased compartmentalization and that these segregate into sublayers (Hoerder‐Suabedissen and Molnár, 2015). In the adult brain, Belgard et al (2011) produced the first transcriptomic atlas of the mouse cortical layers and provided a transcriptomic comparative gene expression analysis to obtain expression profiles of 5,130 highly transcribed genes (Belgard et al, 2013) in a set of structures that develop from one of four sectors of the pallium (medial, dorsal, lateral, and ventral) in the adult mouse and chicken brain. This recent large‐scale transcriptomic analysis reveals expression similarity across chicken and mouse between homologous telencephalic structures such as striatum and hippocampus, but a mostly divergent pattern in other telencephalic compartments (Belgard et al, 2013; Fig.…”

Cellular diversity of the somatosensory cortical map plasticity

“…Electrophysiologically, cortical lamina have since long been shown to display distinct phenotypes in cortical map plasticity (Diamond et al, 1994), stemming from the organization of their thalamic and cortical inputs and their cellular populations (Molyneaux et al, 2007). Cortical laminae can be readily identified through molecular markers, showing their distinct molecular identities (Belgard et al, 2011;Molyneaux et al, 2007), which likely shows the coherence between a layer's functional role and the molecules required to exert it. This stresses the importance of anatomical resolution when studying experiencedependent plasticity on either the electrophysiological and molecular level.…”