Fig. 2

Single cell nucleus RNAseq of the cingulate cortex in Control and HD. a Experimental scheme; first, cingulate cortex was dissected, nuclei were extracted and visualized using DAPI nuclear stain under a fluorescence microscope to ascertain membrane integrity. The nuclei were subjected to 10X chromium single cell RNAseq workflow involving encapsulation of nuclei in oil droplets along with enzymes and barcoded beads, followed by cDNA synthesis and library preparation, and finally, sequencing. b Three-dimensional t-distributed stochastic neighbor embedding (tSNE) plot showing individual nuclei (Points, n = 4786) colored as red (Control) or blue (HD), reduced into three dimensions. c Three dimensional tSNE plot showing the classification of the nuclei into neurons (Cyan), Oligodendrocytes (Green), Astrocytes (Orange), Oligodendrocyte precursor cells (OPC- Black), Microglia (Magenta), and endothelial cells (Purple). d Gene expression heat map of z-scaled normalized counts showing nuclei (Columns) and specific cell-type markers (Rows), a subset of which are shown on the right. Condition (Con versus HD) and Cell-types are color-coded on the top as in panels b-c