Fig. 2: Correlative dSTORM and platinum replica EM analysis of proteins on DCVs.

Correlative images of PC12 cells expressing NPY-mNG and Alexa Fluor-647-GFP-nanobody labeled dark GFP fused proteins a Rab3a, b Rab27a, c Rabphilin3a, and d Granuphilin-a. e Correlative image for endogenous Rim2 labeled with anti-Rim2 antibody. Scale bars are 500 and 200 nm for left and right panels, respectively. Images were cropped from larger images shown in Supplementary Fig. 11. For analysis, ten-pixel-sized bins created from the center of the f EM image and applied to the respective g super-resolved fluorescent image to plot fluorescence profiles. Yellow circle indicates the outline of vesicle, and pink and blue lines are bins within and outside of the vesicle edge. h Averaged and normalized fluorescence intensity profiles for dGFP-Rab3a (n = 8 cells; 458 vesicles), dGFP-Rab27a (n = 7 cells; 545 vesicles), dGFP-Rabphilin3a (n = 8 cells; 644 vesicles), dGFP-Granuphilin-a (n = 10 cells; 275 vesicles), and anti-Rim2 (n = 5 cells; 129 vesicles) (Supplementary Table 1a). Overexpression CLEM data were collected from two (Rab3a, Granuphilin-a) and three (Rab27a, Rabphilin3a) independent experiments and immunolabeled CLEM data from one experiment. The mean fluorescence intensity is shown as a dark line (black = Rab3a; red = Rab27a; blue = Rabphilin3a; magenta = Granuphilin-a), and the standard error of the mean is shown in transparency. The fluorescence intensity profiles for endogenous proteins including Rab3a, Granuphilin-a, and Rim2 are presented in Supplementary Fig. 5.