Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing
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1 SUPPLEMENTARY INFORMATION Resource In the format provided by the authors and unedited. Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing Hannah Hochgerner 1,2, Amit Zeisel 1,2, Peter Lönnerberg 1,2 and Sten Linnarsson 1,2 * 1 Division of Molecular Neurobiology, Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden. 2 Science for Life Laboratory, Solna, Sweden. Hannah Hochgerner and Amit Zeisel contributed equally to this work. * sten.linnarsson@ki.se Nature Neuroscience Nature America Inc., part of Springer Nature. All rights reserved.
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3 Supplementary Figure 1 Overview of sampling and technical details for Data sets A C. (a) Schematic over the dentate gyrus granule layer emergence and maintained neurogenesis through development, as in Fig. 1a, with sampling timepoints indicated for each dataset. (b), (d), (f) Distribution of cell-type frequency in each dataset. Circle area represents fraction of positive cells, per sampling age, normalized by cell-type. Dashed box indicates time points sampled in the hgfap:gfp reporter mouse, by FACS on GFP+ cells. (c), (e), (g) Technical specifications of the datasets. Single-cell barplots for number of molecules (left) and genes (right), arranged by cluster. tsne visualizations of each dataset (compare Fig. 1, Suppl. Fig. 5, Fig. 5), are colored by number of genes (grey-low, red-high).
4 Supplementary Figure 2 Cajal Retzius cells (CR) in the marginal zone of the dentate gyrus. (a) t-sne visualization of Dataset A (see Fig. 1). Cells are stained for expression of genes enriched in the Cajal-Retzius population (grey, low; red, high). (b) Allen Mouse Brain Atlas images of known Cajal-Retzius cell marker Reln (encoding reelin, co-expressed in hilus GABAergic neurons), and more specific genes identified in our dataset Lhx1 and Lhx5, across postnatal development and the adult. Scale bars represent 200μm. Image credit: Allen Institute. (c) Validation of Reln+/Lhx1+ Cajal-Retzius cells (outlined by solid circles) at ages P10, P16, P24 and P37, representative images from hybridizations on six sections in two mice per time point. Higher density of Cajal-Retzius cells along the marginal zone (dashed line) observed in younger ages. Co-expression of Reln/Lhx1 is preserved also in the adolescent. Left panel: Overview dentate gyrus, localization of Cajal-Retzius cells to the marginal zone. Middle panel: Zoom-in on area outlined by solid rectangle in left panel, spanning marginal zone (dashed line), molecular layer and granule layer (between solid outlines). Right panel: detailed view, zoom-in on area outlined by solid square in left panel. Scale bars represent 200μm (left panel) and 50μm (zoom-ins, middle and right panels). (d) Distribution of Cajal-Retzius cells in single-cell data from Dataset A (left) and B (right), across ages, shows enrichment in earlier postnatal time points.
5 Supplementary Figure 3 Early neurogenesis markers. t-sne visualization of Dataset A (as in Fig. 1), cells are stained for expression of consecutive markers of early neurogenesis. Grey - low expression, red - high expression.
6 Supplementary Figure 4 Mutual KNN graph of early neurogenesis, without nipc-specific genes. Analysis of astrocytes and early neurogenesis clusters (Radial Glia-like (n=165), nipc (n=88), Neuroblast 1 (n=97) and 2 (n=777)) with nipc-specific genes removed (see Methods, as in Fig. 2e-f). Nodes represent cells (total n=1127 cells), edges connect mutual nearest neighbors. (a) Cells stained by cluster annotations as in Fig. 1d. nipcs fall along a trajectory between Radial Glia-like and Neuroblast 1. (b) Mutual KNN graph stained by gene expression: progenitor genes (top), cell-cycle genes (middle), neurogenic genes (bottom) (grey, not expressed; red, expressed; compare Fig. 2f). Line indicates the divide of nipcs by distance from Radial Glia-like or Neuroblast 1 (as in Fig 2e).
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8 Supplementary Figure 5 Time-resolved dentate gyrus Data set B and characterization of hgfap:gfp reporter mice. (a) t-sne visualization of all 2303 cells, colored and labeled by cluster names. (b) Heatmap of 17 clusters from 2303 cells (all sampled time points), by their top marker genes (526 genes), expression normalized by gene. Barplots on top show sampling age source. (c) Dendrogram and correlation heatmap of clusters. (d) t-sne visualization (as in (a)). Cells are colored by sampling age and experiment source (hgfap:gfp sorted by FACS). Dashed box indicates astrocytes and clusters in early neurogenesis. (e) t-sne visualization (as in (a)) with cells contributed by FACS are colored light green, cells expressing at least one molecule of Gfap or Cdk1 are encircled as indicated. Dashed circles outline populations that contain GFP+ cells, and are labeled by cluster name. (f) Analysis of clusters containing GFP+ cells. GFP expression is not restricted to Gfap+ cells or progenitor populations. Left: Contribution of GFP+ cells to each cluster, in percent. Line shows total contribution of GFP+ cells to the dataset (5.2%). Left center: Percentage of all cells expressing at least one molecule Gfap, per cluster. Right center: Percentage of GFP+ cells expressing at least one molecule Gfap, per cluster. Right: Percentage of all cells expressing at least one molecule Cdk1, per cluster. (g) Immunohistochemistry of hgfap:gfp mouse dentate gyrus, stained with antibodies against GFP, GFAP, Aldoc (astrocytes) and Pdgfra (OPCs), representative images from stainings in two mice. Left panel: Overview of denate gyrus. Right panel: zoom-in, coexpression of respective markers indicated by arrowheads. Scale bars represent 200μm (left) and 50μm (zoom-ins, right).
9 Supplementary Figure 6 Markers of neurogenesis, maturation, and Notch-signaling. t-sne visualization of Dataset A (as in Fig. 1d), cells stained for expression of markers of early neurogenesis (Calb2), granule cell maturation (Fxyd7-Icam5), and Notch-signaling related genes (Notch1, Notch2, Dner, Dlk2, Jag1). Grey, low expression; red, high expression.
10 Supplementary Figure 7 Overview of dentate gyrus Data set C, spanning perinatal, juvenile, and adult neurogenesis. (a) t-sne visualization of all 24,185 cells, colored and labeled by cluster names, sampled from perinatal (E16.5-P5), juvenile (P18-23) and adult (P ) mice. (b) Dendrogram and correlation heatmap of Dataset C clusters. (c) Heatmap of 24 clusters from 24,185 cells (all sampled time points), represented by their top marker genes (756 genes), expression normalized by gene. Barplots on top show sampling age source.
11 Supplementary Figure 8 Suggested model of cell types involved in perinatal and adult dentate neurogenesis. Both in perinatal and adult neurogenesis we propose distinct initiation clusters (radial glia and radial glia-like; size of circle symbolizes frequency), and convergence of the maturation process.
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Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
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