The spinal cord injury (SCI) myeloid cell atlas is a shiny web app-based resource that can be used to interactively browse and download the data from:

Hamel R, et al. Time-resolved single-cell RNAseq profiling identifies a novel Fabp5-expressing subpopulation of inflammatory myeloid cells in chronic spinal cord injury. bioRxiv 2020.2010.2021.346635 (2020)


Innate immune responses following spinal cord injury (SCI) participate in early secondary pathogenesis and wound healing events. Here, we used time-resolved scRNAseq to map transcriptional profiles of SC tissue-resident and infiltrating myeloid cells post-SCI. Our work identifies a novel subpopulation of Fabp5+ inflammatory myeloid cells, comprising both resident and infiltrating cells and displaying a delayed cytotoxic profile at the lesion epicentre, which may serve as a target for future therapeutics.

Experimental Design

Using the 10X Genomics Chromium platform, we single cell RNA-sequenced 30,958 myeloid cells from female and male mice at 1, 2, 3, 10, and 21 days post contusion SCI injury. We used laminectomy only mice as controls. The data was collected from the Cx3cr1CreERT (Cx3) mouse model, which labels all myeloid lineage cells with YFP, and from the Cx3cr1CreERT x tdTomato (Cremato) mouse, which labels resident myeloid cells as RFP+ YFP+, and infiltrating myeloid cells as RFP- YFP+ .



Please contact Regan Hamel ( with any web atlas-related queries or suggestions.

Select one of the following options to colour the reference plot

Input the gene of interest to visualize on the plot. To visualize the average expression of a set of genes, separate each gene with a comma (max 50 genes)


Download: Click the download button to save a pdf file of the plot(s)

Gene Expression: Depicted as the log2 transformed, normalized UMI counts per cell


HC = healthy control (laminectomy only); MG = microglia; MCd = monocyte derived macrophages; DC = dendritic cells; NP = neutrophils