Resources

This Resource article provides detailed expression data from the striatum and cerebral cortex of early prenatal human samples, ranging in age from 2 to 20 weeks post-conception. Using a number of different analyses, the authors describe the transcriptional, spatio-temporal expression and functional profile that distinguish human striatal from neocortical neurons while also elucidating some differences between human and mouse striatal development.

Expression quantitative trait loci (eQTLs) are genomic regions that regulate gene expression. Here the authors provide a publicly available data set of exon-level eQTLs across the human brain. This includes many genome-wide association study (GWAS) hits for neurological and psychiatric disorders.

In this resource, the authors provide a comprehensive map of the thalamocortical projections in the mouse brain. To do this, they employed 254 highly overlapping injections of viral vectors to label and characterize long-range projections. Using this map as a framework, the authors determine the functionality of a subset of these connections via expression and activation of channelrhodopsin.

Microglia are resident myeloid cells of the central nervous system integral for neuroprotective and neurodegenerative processes. Here the authors describe a unique TGF-β dependent molecular and functional microglia signature that distinguishes these cells from other immune and glial cells in the periphery and brain.

In this Resource, the authors generate a genome-wide methylation profile of DNA from the normal-appearing white matter of control and multiple sclerosis–affected brains and find subtle, but widely distributed, differences. In particular, they report that hypermethylated genes that regulate oligodendrocyte survival are also transcriptionally downregulated.

In this Resource study, the authors used Direct RNA Sequencing (DRS) to quantitatively examine the transcriptional profile of microglia, focusing specifically on the proteins important for binding endogenous ligands and potential pathogens—a collection they term the 'sensome'. They also compare this profile to that of peripheral macrophages.

Using whole-transcriptome RNA sequencing at single-nucleotide resolution, this Resource article describes the mRNAs, RNA editing, splice variants and exon-intron boundaries of expressed genes in the cerebral cortex of embryonic and adult mice.

In this Resource study, the authors used high-resolution mass spectrometry to elucidate the precise proteomic complement of the inner ear hair bundle. Many of the proteins that are enriched in the hair bundles are encoded by known deafness-associated genes.

This study describes the generation of knock-in mouse lines that express optogenetic activators or silencers in a CRE recombinase–dependent manner, and demonstrates the reliability and utility of these tools with in vivo and ex vivo light-induced activation and silencing of neuronal activity.

Using several lines of retinal cell type–specific GENSET BAC transgenic GFP mice, the authors segregated these retinal cell types then subjected them to transcriptome microarray analysis to provide a transcriptional 'barcode' of retinal cell identity.

DNA methylation in the context of epigenetics occurs on the 5' position of cytosine, which can be further oxidized by enzymes from the Ten-eleven translocation (Tet) family, resulting in 5-hydroxymethylcytosine (5-hmC). In the context of embryonic stem cells, Tet and 5-hmC DNA act in an alternate epigenetic state that regulates epigenetic programming and stem cell differentiation. Here, the authors describe the epigenomic profiling of 5-hmC in mouse and human brain across different time periods during development and aging.

It has been unclear how extensively neuronal DNA methylome is regulated by activity. In this resource article, the authors use next-generation sequencing methods and quantitatively compare the CpG methylation landscape of adult mouse dentate granule neurons in vivo before and after synchronous neuronal activation.

This Resource chronicles dynamic gene expression patterns in the developing hypothalamus from embryonic day 10.5 through maturity. The authors find that Shh must be expressed in the hypothalamic basal plate for differentiation of the anterior and tuberal hypothalamic nuclei.

This Resource paper describes a set of five new reporter mice, derived from Rosa26, driving Cre-dependent strong and ubiquitous expression of fluorescent proteins. In particular, the new mice show clear and specific expression patterns in the adult brain. The mice are available through Jackson Laboratories, and growing expression datasets can be accessed at http://transgenicmouse.alleninstitute.org/.

Selective targeting of specific neuronal populations, for genetic or other manipulations, is crucial to much of neuroscience. The authors screened 536 BAC transgenic mouse lines from the GENSAT collection for specific reporter expression in the retina. Here, they describe several mouse lines selectively targeting different retinal cell types. The full dataset is accessible at http://www.gensat.org/retina.jsp.

This resource article describes a bioinformatical tool that, accessing an extensive gene expression database, allows the definition and identification of new brain structures based on gene expression patterns.