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. Author manuscript; available in PMC: 2022 Apr 4.
Published in final edited form as: Nat Methods. 2021 Oct 4;18(10):1204–1212. doi: 10.1038/s41592-021-01278-1

Figure 3. InCITE-seq measures changes in nuclear TF levels after stimulation of the mouse hippocampus.

Figure 3.

a. UMAP embedding of inCITE-seq nuclei (as in Fig. 2b) colored by c-Fos protein levels (nADT, color scale from 5th to 95th percentile). Distribution of c-Fos (b,c) or p65 (d) protein levels (nCLR, x axis) shown as a kernel density estimate in neurons of KA vs. PBS treated mice (b, P=10−15, two-sided KS test), in granule cells (GC) vs. cornu ammonis (CA) neurons in KA treated mice (c, P=1.7*10−7, two-sided KS test), or in neurons of KA vs. PBS treated mice (d, not significant; P=0.15 two-sided KS test). e,f,g. Immunofluorescence stain of the hippocampus after PBS (gray border) or KA (green border) treatment; representative of 3 independent experiments. Major hippocampal features denoted: dentate gyrus (DG), cornu ammonis (CA). e. Stain of c-Fos (red), NeuN (green), and DAPI (blue). Left: scale bar, 600μm. Right: close-up of the DG (dashed box) shows heterogeneity in c-Fos intensity; scale bar, 100μm. f. Stain of SST (red), c-Fos (green), and DAPI (blue). Left: scale bar, 100μm. Right: close-up of the DG (dashed area box); scale bar, 30μm. g. Immunofluorescence stains of p65 (red), NeuN (green), and DAPI (blue), PBS or KA treatment. Left: all stains. Right: p65 stain. Scale bar, 100μm. h. Distribution of mRNA levels (Z score of log-normalized counts, y axis) in nuclei with high or low levels (defined in Extended Data Fig. 6) of the encoded protein (x axis) under PBS (gray) or KA (green) treatment. Boxplot: centre line indicates median, box bounds represent first and third quartiles, whiskers span from each quartile to the minimum or the maximum (1.5 interquartile range below 25% or above 75% quartiles). Dots: nuclei with non-zero mRNA levels measured across n=2 biologically independent samples, with 1,696 nuclei, 214 nuclei, and 653 nuclei shown for Fos, Rela, and Rbfox3, respectively. Significance, from bottom-left to top-right: P=2*10−6, P=9*10−5, P=4*10−6, P=9.7*10−3, two-sided Mann-Whitney test. NS – not significant.