Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system

Abstract

The Allen Brain Atlas (http://www.brain-map.org) provides a unique online public resource integrating extensive gene expression data, connectivity data and neuroanatomical information with powerful search and viewing tools for the adult and developing brain in mouse, human and non-human primate. Here, we review the resources available at the Allen Brain Atlas, describing each product and data type [such as in situ hybridization (ISH) and supporting histology, microarray, RNA sequencing, reference atlases, projection mapping and magnetic resonance imaging]. In addition, standardized and unique features in the web applications are described that enable users to search and mine the various data sets. Features include both simple and sophisticated methods for gene searches, colorimetric and fluorescent ISH image viewers, graphical displays of ISH, microarray and RNA sequencing data, Brain Explorer software for 3D navigation of anatomy and gene expression, and an interactive reference atlas viewer. In addition, cross data set searches enable users to query multiple Allen Brain Atlas data sets simultaneously. All of the Allen Brain Atlas resources can be accessed through the Allen Brain Atlas data portal.

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA–tRNA interface

“…During early development, the embryonic liver is a haematopoetic organ; at birth, the neonatal liver becomes the primary metabolic and detoxification organ (Si-Tayeb et al 2010); at weaning, further metabolic pathways are up-regulated (Bohme et al 1983;Girard et al 1992). In the developing brain, coordinated gene expression changes in a heterogeneous collection of diverse cell types shape the functional specialization of specific regions in both embryonic and postnatal brains (Liscovitch and Chechik 2013;Sunkin et al 2013).…”

“…The direct interaction of these transcripts produced by Pol II and Pol III is a vital step in the flow of genetic information, in which the triplet codons in mRNAs are selectively identified by their counterpart tRNA anticodons to direct protein synthesis. To explore the largely unknown regulatory mechanisms active at this mRNA-tRNA interface, we exploited the rapid and extensive changes in the transcriptome occurring among different developmental stages of mammalian organogenesis (Kyrmizi et al 2006;Kang et al 2011;Lee et al 2012;Liscovitch and Chechik 2013;Sunkin et al 2013).…”

Expression of ORAI1, a Plasma Membrane Resident Subunit of the CRAC Channel, in Rodent and Non-rodent Species

“…The expression patterns outside the CNS were grossly the same for these two antibodies with the only clear difference in the CNS where mAb266.1 was able to detect ORAI1 protein. The Allen Brain Atlas shows no brain expression using an in situ hybridization (ISH) probe that spans the C-terminal coding region of the protein, and overlaps with the polyclonal antibody binding epitope (Sunkin et al 2013) (Fig. 5).…”

“…The ISH probe for this study has been mapped to its respective protein sequence. The Allen Brain Atlas probe is shown for comparison (Sunkin et al 2013). limit of ISH; therefore, results across tissues may be inconsistent using this method.…”

Technologies of High-Throughput Tissue-Specific Gene Expression Profiling

“…Fluorescence in situ hybridization (FISH) [1] uses fluorescent probes to bind specific nucleic acid targets, while immunofluorescence can use fluorophore-linked antibodies to target specific proteins [2] . Recombinant technology allows a fluorescent protein to ligate covalently to the product of target gene [3,4] .…”