Quick Facts 
Species: Mus musculus (10090) 
Strain: C57/BL6 
Anatomical Region: SNr, SNc, VTA 
Brain ID: MD720 
Contact: Velina Kozareva vkozarev@broadinstitute.org

This study is a part of the NIH's Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative - Cell Census Network (BICCN). Specifically, as a part of the Comprehensive Center for Mouse Brain Cell Atlas (Read more, associated RFA here), this study is one of a series of studies that connects anatomical data (from the Brain Architecture Architecture portal) with molecular measurements (found here in Single Cell Portal Studies). 

In this study, we show gene expression for 13861 nuclei from the SNr, SNc, VTA anatomic regions of the mouse brain. These data were generated using single nuclei RNA-seq leveraging the 10X 3’ sequencing assay. Anatomical regions were prepared by cryosectioning via 20um tape transfer proceeding in an anterior-posterior progression until the start site (anterior Bregma level) of the Anatomical Tile (AT) punch site was reached. During this, the technician is aided in this by UV visualization of the fiber tracts in the block face and direct comparison to the Allen Mouse Brain atlas. Six consecutive 100 um thick sections were cryosectioned onto tape, and punched out as specified to total 600um of A-P thickness. Punch diameters may be 1.5mm, 1mm or 0.5mm, and some targets may require multiple small punches to match their anatomical shape.  The remnants of punched thick sections were then nissl stained and registered to verify the contents of each AT collected.

Using standard graph-based clustering methods, we have identified 8 major cell types that can be explored here. The corresponding sections and punches pooled in this study can be viewed on the Brain Architecture portal through the links shown above.

All available MD720 studies: