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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 4: Slide-seq identifies local transcriptional responses to injury:

Figure 4:

(A) Top: All mapped beads for a coronal hippocampal slice from a mouse sacrificed 2 hours after injury, with circle radius proportional to transcripts. Bottom: genes marking the injury. (B) As in (A), for a mouse sacrificed 3 days after injury. Top and middle right: DAPI image of an adjacent slice. Panels with black backgrounds show NMFreg cell types as density plots. Scale bar: 250 μm (6). (C) As in (B), for a mouse sacrificed 2 weeks following injury. Bottom scale bar: 500 μm. (D) Spatial density profiles for the puck in (B) (6). (E) Spatial density profiles for the puck in (C). Lyz2 is plotted as a marker of macrophages. The vertical axis in (D) and (E) represents cell-type density in arbitrary units (6). (F) The thickness of the features in (D) and (E) (mean ± std., N=6 for scar, N=6 for penetration, N=3 for mitosis layer). (G-J) Gene ontology-derived metagenes for the puck in (B) (top) or (C) (bottom). Warmer colors correspond to greater metagene counts. (K) The IEG metagene (Table S2) for two 2-week pucks. Circular images in (A-C) refer to the scale bar in (A). All scale bars for images with blue backgrounds 500 μm. Red arrows indicate the injury.