(A) Confocal images showing expression of the nuclear envelop protein Unc84-GFP in the antenna driven by elav-GAL4 and AM29-GAL4; anti-GFP labeling is in green and anti-Elav (pan-neuronal nuclear marker) labeling is in magenta. Scale bar, 20 µm. (B–C) Box plots showing distribution of uniquely-mapped reads [average reads are, 24 hr APF cells (exon): 8.4 × 105; 24 hr APF cells (exon + intron): 9.4 × 105; 24 hr APF nuclei (exon): 7.4 × 105; 24 hr APF nuclei (exon + intron): 1.1 × 106; adult (exon): 3.6 × 105; adult (exon + intron): 5.0 × 105] (B) and genes detected [average genes detected are, 24 hr APF cells (exon): 1,706; 24 hr APF cells (exon + intron): 1,847; 24 hr APF nuclei (exon): 520; 24 hr APF nuclei (exon + intron): 714; adult (exon): 956; adult (exon + intron): 1,135] (C) per cell/nucleus in ORNs. These plots depict a breakdown of all cells/nuclei with exonic reads only and exonic and intronic reads combined. Analyses in Figure 2 and the rest of the study were performed on cells with exonic reads only and nuclei with combined exonic and intronic reads. (D–E) Stacked bar plots of proportion of exonic and intronic reads in scRNA-seq and snRNA-seq samples where reads were combined in ORNs (D) and PNs (E). (F–J) Top 20 transcripts with highest percentage of total reads in 24 hr APF ORN cells (F), 24 hr APF ORN nuclei (G), adult ORN nuclei (H), adult PN cells (I), and adult PN nuclei (J). Note that top transcripts in adult ORN nuclei contain mitochondrial (mt) transcripts, likely artifacts resulting from dissociation procedures. Transcripts shared between stage-matched cells and nuclei are in red. (K–L) Gene Ontology (GO) analysis based on genes enriched in 24 hr APF ORN cells compared to 24 hr APF ORN nuclei (K) and adult PN cells compared to adult PN nuclei (L). The top 13 significant GO terms are shown. Approximately500 DE genes were used for GO analysis in each category. Bolded terms in the cell categories are shared between ORN and PN cells. (M–N) Violin plots showing cell-enriched (M) and nucleus-enriched (N) transcripts in each category in 24 hr APF ORNs. Note that mitochondrial genes are more enriched in cells, whereas long non-coding RNAs are more enriched in nuclei. (O) Heatmap depicting Obp expression in adult ORN nuclei. The y-axis is arranged according to descending order of Obp expression levels from bulk RNA-sequencing from the antenna (Menuz et al., 2014). Highest detected Obps in Menuz et al. are expressed at levels 10–15 times higher than the highest detected chemosensory co-receptor, Orco. In situ expression analysis suggests that Obps are mostly expressed in supporting cells (Larter et al., 2016); thus, the correlation of Obp expression levels from previous study and the expression patterns shown here suggest that Obp expression seen here is likely due to contamination of highly abundant ambient RNAs associated with neuronal nuclei.