There are 100 million cells in the adult mouse brain, composed of an unknown number of specific types. The systematic identification, characterization and positional mapping of these cell types could reveal fundamental organizing principles of the mammalian nervous system, and will provide an invaluable resource for molecular and circuit neurobiology. One of the most difficult and important challenges for the Brain Initiative Cell Census Initiative (BICCN) will be robustly associating transcriptional data on cell types to the anatomy at the proper scale. Because of the large throughput and the ease of biologically interpreting gene expression signals, the BICCN single-nucleus/single-cell dataset is expected to be foundational for defining cell types and states in the profiled tissues.
Here we present a molecular atlas of the mouse brain with three major attributes: gene expression patterns and signatures that define specific cell types; an accurate census of each cell type’s proportional representation; and spatial localization of these types on a reference brain.
Our team has pioneered advances in nucleic acid sequencing and the preparation of gene expression profiles from individual cells and nuclei making it technically feasible to systematically sample the cellular diversity of an entire complex tissue such as the mouse brain. We are assembling a high-coverage mouse brain molecular atlas by profiling single cells through novel droplet-based single-cell and single-nucleus RNA sequencing technology and then spatially registering these cells to their source regions in a reference brain.
Our strategy combines reproducible sampling of defined anatomical samples or “tiles” of biological interest using the tape-transfer method for performing serial sectioning of frozen tissue blocks. In this method, thin tissue sections are adhered to a piece of adhesive tape, permitting physical manipulations of the tissue while maintaining the physical and geometrical integrity of the tissue. Small portions of tissue are physically removed from the adhered tissue sections using a biopsy punch, and the remainder of the section, as well as all other sections without punches, are tape-transferred onto glass slides and Nissl stained. The resulting image stack is reassembled into a 3D stack that is atlas mapped using diffeomorphic coordinate transformations.