Extended Data Fig. 3: PL-CLIP identifies properties of dendritic RNAs in resting and depolarized neurons.

a, Length and (b) GC content of resting and depolarized PL-CLIP-enriched dendritic RNAs and all detected RNAs in cortical neurons (‘All’, n = 17,654) are compared. Colors: salmon (resting, n = 2,788); burgundy (depolarized, n = 3,727). Significance was calculated by the two-sided Wilcoxon signed-rank test. Box plots show lower and upper hinges corresponding to the first and third quartiles (representing 25th and 75th percentile, respectively). Whiskers extend from the hinge to the 1.5x interquartile range. The center line indicates the median. P values: all significance values reported are < 2.2e-16 except for Transcript length (Rest vs. Dep = 4.18e-15), CDS (Rest vs. Dep = 0.081), 5′UTR (All vs. Rest = 2.10e-8; All vs. Dep = 4.22e-10; Rest vs. Dep = 0.93), 3′UTR (All vs. Rest = 0.15). c, RNA fluorescence in situ hybridization (RNA-FISH) combined with MAP2 IF to show dendrites and dendritically de-enriched (Snca) and enriched (Kmt2d, Map2 and Dlg4) RNAs by resting PL-CLIP. Images are quantified on the right (n = 3). Significance was derived from biological replicates, showing the center line at median and using the two-tailed, paired Student’s t-test. d, RNA-FISH combined with IF showing dendritic (MAP2-green) localization of Rapgef4 (red) and Ppp1r9b (white) in resting and depolarized neurons, (e) quantified for soma and dendrites. 4 fields of images per replicate for n = 2 presented as mean ±s.d. All images are taken at ×40 magnification, except for Dlg4, which was taken at ×60. P values: ns (not significant) >0.05; * <0.05; ** <0.01; *** <0.001; **** <0.0001. Scale bars, 100 μm. n indicates the number of biologically independent samples.