Fig. 1: A glia-enriched multimodal cell census of the injured spinal cord.
From: The regulatory code of injury-responsive enhancers enables precision cell-state targeting in the CNS
a, Schematic workflow of the multiomic experiment. Mice were subjected to a contusion injury to the spinal cord, and tissue was collected at different time points after the injury, as well as from uninjured controls. We isolated nuclei from whole tissue (unsorted) as well as from samples enriched in less abundant cell populations using flow cytometry: neuron and oligodendroglia depleted (NEUN−SOX10−) or ependymal cell enriched (Foxj1–tdTomato (Foxj1–Tom)). The nuclei were then profiled at the multiomic level (ATAC + RNA) to investigate injury-responsive gene regulatory programs; SCI, spinal cord injury. b–d, Uniform manifold approximation and projection (UMAP) visualization and clustering calculated on multiomic (b), gene expression (c) and chromatin accessibility data (d); wnn, weighted nearest neighbor; pca, principal component analysis; lsi, latent semantic indexing. e, Heat map displaying clustering agreement, in proportion, between analyses computed on multiomic and gene expression data (top), and multiomic and chromatin accessibility data (bottom). The number of populations identified at the same clustering resolution is reported in parentheses for each modality. f,g, Heat map displaying average scaled data for significantly enriched genes (f) and peaks (g) for each cluster identified at the multiomic level. Colored bars represent cell types (top) and subtypes (bottom). h, Coverage plots from examples of enriched peaks across the multiomic clusters. On the left, bar plots display cluster size (×1,000), whereas on the right, tracks are grouped according to cell type. i, Feature plot displaying gene expression levels for Sox2. j, Heat map representing average scaled accessibility across glia cells for peaks linked to Sox2 (peak-to-gene (PtoG) links). k, Coverage tracks for the Sox2 transcription start site (TSS), along with distal regions enriched in different glial cells. Distance from the TSS (in kilobases (kb)) is reported below the plots.
