[Figure 5 - supplemental] Nuclear proportion estimates are supported by multiple genes and consistent with previously reported values. (A) Box plots of log2-transformed expression of two nuclear transcripts, Meg3 and the small nucleolar RNA Snhg11, in matched nuclear and cell clusters. (B) Representative sections of VISp from three Cre-driver mouse lines with layer boundaries, nuclei labeled with DAPI (blue), and subsets of neurons labeled with tdTomato (red). Scale bar is 100 µm. (C) Nucleus and soma area measurements from three Cre-lines, and linear regressions to estimate nuclear proportions. (D) Left: Section of VISp from wild type mouse labeled with DAPI and Neurotrace 500 fluorescent Nissl stain with layer boundaries indicated by white lines. Scale bar is 100 µm. Right: Nuclear proportion was quantified based on nucleus and soma area measurements and plotted as a function of cortical depth. Size and darkness of points are proportional to soma area. (E) Average nuclear proportions of 4,373 genes (mostly house-keeping) also expressed in mouse pancreatic beta-cells and liver cells \cite{Halpern2015} are moderately correlated with and approximately 13% less than estimated proportions in this study. (F) The distributions of nuclear proportions are highly similar with slightly higher reported cytoplasmic enrichment for reported genes. Note that the matched set of genes includes 99% protein-coding genes so the distributions more closely resemble those genes in Figure \ref{886252}D.