Fig. 5

Comparison of single-cell transcriptomes from circulating and infiltrated human immune cells highlights the influence of the lesion microenvironment on cell states. A and B Annotated UMAP (A) and MetaCell (B) plots of all cells present within SCI blood (left) and cord (right) samples. C Proportion of cell type / clusters out of all cells present. D Number of differentially expressed genes (DEGs) either down- or upregulated (red) in human immune isolated from the spinal cord versus blood. E Heatmap showing gene expression of the top-10 genes that were either down- or upregulated in human immune cells that were isolated from the injured spinal cord. F Number of DEGs (i.e., markers; left) and GO terms (right) for each cell cluster between compartments (i.e., cord v blood). Blue represents terms downregulated and red represents terms upregulated in the huCD45 + cells from spinal cord compared to blood samples. G Top GO terms enriched for each cluster. Red colour in GO plot represents –log10(adjusted p-value) for upregulated genes/terms, while blue colour the log10(adjusted p-value) would represent downregulated genes/terms; dot size represents ratio of genes contributing to the GO term