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. 2021 Jan 6;10:e63092. doi: 10.7554/eLife.63092

Figure 2. The dendritic transcriptome of GABAergic interneurons.

(A) Plots showing the average normalized unique molecular identifier (UMI) counts of genes detected in the dendrites (≥1.9 molecule per sample on average) of the indicated cell types. X-axis shows genes ranked according to their expression from lowest to highest. Some genes are indicated by name. N = glutamatergic (11), GABAergic 1 (36), GABAergic 2 (30), and GABAergic 3 (18). (B) Same as A but for somatic samples. N = glutamatergic (95), GABAergic 1 (103), GABAergic 2 (82), and GABAergic 3 (65). (C) smFISH for indicated mRNAs (in white) observed in GABAergic dendrites immunolabeled with an anti-Map2 antibody (magenta). GABAergic identity was determined by smFISH Gad1/2 as seen in Figure 2—figure supplement 1A. Scale bar = 10 µm. (D) Raster plot showing smFISH dendritic detection pattern over a large number of dendrites. Dendrites of both excitatory and inhibitory cells were straightened from the same images, sorted according to the expression of Gad1/2 (positive below red line, negative above red line) and the gene of interest channel displayed, after automated peak detection, as a raster plot.

Figure 2.

Figure 2—figure supplement 1. Cell type-specific effects in the dendritic transcriptome.

Figure 2—figure supplement 1.

(A) Gad1/2 expression (green) as determined by smFISH. Images from double smFISH with respective gene. See expression of respective gene in 2C. (B) Density of puncta (puncta/10 µm) in distal dendrites for gene of interest, in Gad1/2 positive or negative neurons as determined by double smFISH. (C) Density plots showing distribution of p-values in comparisons between the real members of each group, 1000 mock comparisons after random reshuffling, and the average of the mock comparisons. (D) Cumulative distribution of the mock permutation average was used to identify the p-value in which a 5% false discovery rate was observed for each comparison. The cumulative distribution of the real comparison is also shown as reference. (E) Diagram showing the hierarchy of cell types established in clustering analysis (see Figure 1D).