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. Author manuscript; available in PMC: 2020 Mar 29.
Published in final edited form as: Science. 2019 Mar 28;363(6434):1463–1467. doi: 10.1126/science.aaw1219

Figure 2: Localization of cell types in cerebellum and hippocampus using Slide-seq.

Figure 2:

(A) Schematic for assigning cell types from scRNA-seq datasets to Slide-seq beads using NMF and NNLS regression (NMFreg). (B) Loadings of individual cell types, defined by scRNA-seq cerebellum (9) on each bead of one 3 mm-diameter coronal cerebellar puck (red, cell type location, gray, Purkinje loadings plotted as a counterstain). Other cell types are in Fig. S6. (C) Left: Number of cell types assigned per bead (Fig. S3). Right: The number of beads called as each scRNAseq-defined cell type for cerebellar pucks (mean ± std. N=7 pucks). (D) Projections of hippocampal volume with NMFreg cell type calls for CA1 (green), CA2/3 (blue) and dentate gyrus (Red). Top left: Sagittal projection. Top right: Coronal projection. Bottom left: Horizontal projection. Bottom right: axis orientations for each of the projections. (E) Composite image of metagenes for six different cell types. All scale bars 250 μm. All metagenes are listed in Table S2.