[Figure 4 - supplemental] Nuclear and cell clusters are well matched based on marker gene expression. (A) Pairwise correlations between previously reported mouse VISp cell type clusters \cite{Tasic2016a} and nuclear and cell clusters using average cluster expression of the top shared marker genes. Heatmaps show remarkably similar correlation patterns, supporting the existence of a well matched set of nuclear and cell clusters. Nuclear and cell clusters were annotated based on the reciprocal best matching published cluster name and mapped to two interneuron types and five of eight layer 5 excitatory neuron types. (B) Comparisons of the proportion of nuclei or cells expressing marker genes (CPM > 1) for matched pairs of clusters. Correlations are reported at the top of each scatter plot, and cell type specific markers are labeled. As expected based on Figure \ref{835862}C, gene detection is consistently higher in cells than nuclei. (C) Matched clusters have similar proportions of nuclei and cells (except for two closely related cell types, L5a Hsd11b1 and L5 Batf3), which supports the accuracy of the initial correlation based mapping of single nuclei to cells. (D) Average gene expression quantified based on intronic reads is more highly correlated between cells and nuclei than expression quantified based on exonic reads, particularly for highly expressed genes. Malat1Meg3, and Snhg11 are the three highest expressing genes in nuclei and have consistently lower expression in cells, as expected based on their reported nuclear localization.