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. 2019 Nov 7;8:e47809. doi: 10.7554/eLife.47809

Figure 2. Quantitative analysis of RNA localization.

(A) Scatter plot comparing log mean read counts and log fold difference in projections versus whole cells, for 19,815 RNA transcripts with non-zero read counts. 1440 (orange dots) are significantly enriched (q-value < 0.01 and fold-change > 1.5) in projections, 1486 (blue dots) are enriched in whole cells, and 16,899 (gray dots) show no significant enrichment in either sample. Ribosomal protein encoding RNAs are shown as black dots; rhombi enclose labeled RNAs. (B–G) smFISH validation of examples of projection-localized (B) versus projection-depleted (C), and low (D), medium (E), high (F), and higher (G) abundance mRNAs. Upper left corner shows gene name, lower right corner shows projection:whole cell TPM. Scale bars = 20 μm.

Figure 2—source data 1. Isoform abundances and differential expression analysis output.
Figure 2—source data 2. Sequences targeted by smFISH probes.

Figure 2.

Figure 2—figure supplement 1. Correlation between RNAseq from biological replicates.

Figure 2—figure supplement 1.

Correlation between biological replicates (TPM values) of whole cell and projection RNAseq datasets. The color gradient corresponds to the value of Spearman’s correlation coefficient shown in each cell of the heatmap.
Figure 2—figure supplement 2. Gene ontology classes enriched in projections and whole cells.

Figure 2—figure supplement 2.

Gene ontology classes significantly represented by genes enriched in projections or whole cells. CC = Cellular Component sub-ontology classification.