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Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

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Science  29 Mar 2019:
Vol. 363, Issue 6434, pp. 1463-1467
DOI: 10.1126/science.aaw1219
  • Fig. 1 High-resolution RNA capture from tissue by Slide-seq.

    (A) (Left) Schematic of array generation. A monolayer of randomly deposited, DNA barcoded beads (a “puck”) is spatially indexed by SOLiD sequencing. (Top right) Representative puck with sequenced barcodes shown in black. (Bottom right) Composite image of the same puck colored by the base calls for a single base of SOLiD sequencing. (B) Schematic of the sample preparation procedure. RT, reverse transcription. (C) (Top left) t-distributed stochastic neighbor embedding (tSNE) representation of Slide-seq beads from a coronal mouse hippocampus slice with colors indicating clusters. GD, dentate gyrus. (Right) The spatial position of each bead is shown, colored by the cluster assignments shown in the tSNE. (Bottom left) Inset indicating the position of a single-cell-thick ependymal cell layer (arrows). (D) As in (C), but for the indicated tissue type (see fig. S2 for clustering and cluster identities). All scale bars: 500 μm.

  • Fig. 2 Localization of cell types in the cerebellum and hippocampus using Slide-seq.

    (A) Schematic for assigning cell types from scRNA-seq datasets to Slide-seq beads using NMF and NNLS (non-negative least squares) regression (NMFreg). (B) Loadings of individual cell types, defined by scRNA-seq of the cerebellum (10), 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) Number of beads called as each scRNA-seq–defined cell type for cerebellar pucks (mean ± SD, N = 7 pucks). (D) Projections of hippocampal volume with NMFreg cell type calls for CA1 (green), CA2 and CA3 (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.

  • Fig. 3 Identification of variation in cerebellar gene expression by Slide-seq.

    (A) Heatmap illustrating the separation of Purkinje-expressed genes into two clusters by spatial gene correlation. The i,jth entry is the number of genes found to overlap with both genes i and j in the Purkinje cluster (7). (B) For genes with significant expression (P < 0.001, Fisher exact test) in the nodulus-uvula region (7), the fraction of reads localized to the nodulus and uvula as well as to the VI/VII boundary is shown. Pcp4, a ubiquitous marker for Purkinje cells, is in gray. (C) An Aldoc metagene (cyan); a Cck metagene (red). (D) A H2-D1 metagene (yellow); a Hspb1 metagene (blue). The bottom image is a close-up view of the boxed region. All scale bars: 250 μm. All metagenes are listed in table S2.

  • Fig. 4 Slide-seq identifies local transcriptional responses to injury.

    (A) (Top) All mapped beads for a coronal hippocampal slice from a mouse euthanized 2 hours after injury, with circle radius proportional to transcripts. (Bottom) Genes marking the injury. (B) As in (A) for a mouse euthanized 3 days after injury. (Top and middle right) DAPI (4′,6-diamidino-2-phenylindole) stained image of an adjacent slice. Panels with black backgrounds show NMFreg cell types as density plots. Scale bar: 250 μm (7). (C) As in (B) for a mouse euthanized 2 weeks after injury. Bottom scale bars: 500 μm. (D) Spatial density profiles for the puck in (B) (7). (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 (7). ML, mitotic layer; AS, astrocytic scar; MM, microglia-macrophage distance; MP, microglia penetration. (F) Thickness of features in (D) and (E) (mean ± SD, N = 6 measurements for scar, N = 6 for penetration, N = 3 for mitosis layer). (G to J) Gene ontology–derived metagenes for the puck in (B) (top) or (C) (bottom). (K) The IEG metagene (table S2) for two 2-week pucks. In (G) to (K), warmer colors correspond to greater metagene counts. The 1-mm scale bar in (A) pertains to the circular images in (A) to (C). All scale bars for images with blue backgrounds: 500 μm. Red arrows indicate the injury.

Supplementary Materials

  • Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

    Samuel G. Rodriques, Robert R. Stickels, Aleksandrina Goeva, Carly A. Martin, Evan Murray, Charles R. Vanderburg, Joshua Welch, Linlin M. Chen, Fei Chen, Evan Z. Macosko

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Figs. S1 to S15
    • Tables S1 to S3
    • Caption for Movie S1
    • References

    Images, Video, and Other Media

    Movie S1
    A 3D volume rendering of CA1, CA2/3 and dentate gyrus as shown in Fig. 2. Scale bars: 500 μm.

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