Extended Data Fig. 2: Validation of single cell oxidative stress transcriptome of CNS innate immunity.
From: Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation
a, Flow cytometry plots of live CD11b+ROS– and live CD11b+ROS+ cells from spinal cord of individual healthy and EAE mice. Cell population (%) is shown inside gate. Data are representative of two independent experiments with similar results. b, Representative histogram plots (top) and quantification of mean fluorescence intensity (MFI, bottom) of ROS production (assessed via DCFDA) in CD11b+ cells from healthy and EAE mice. Data are from n = 4 mice per group (a, b) (mean ± s.d.). *P < 0.05 (two-tailed Mann-Whitney test). c, Violin plots of number (n) Gene (nGene) and unique molecular identifiers (nUMI) post-normalization and shown for each biological replicate for scRNA-seq. Data are from n = 2 mice per group. d, Correlation gene expression scatter plot between healthy (left) or EAE (right) biological replicates from scRNA-seq. Data are from n = 2 healthy and 2 EAE mice depicted as the average gene expression for cluster 1 (n = 14,927 and 12,861 genes for healthy replicate 1 and 2 respectively) and cluster 6 (n = 11,856 and 14,319 genes for EAE replicate 1 and 2 respectively) with Pearson correlation coefficients r = 0.98 and 0.99, respectively. e, UMAP plots (left) of each cells sample type and summarized in table (right). f, Violin plots of log expression levels of potential astrocytic (Gfap), neuronal (Tubb3 and Rbfox3), oligodendrocyte (Mog and Plp1) contaminates in each cluster. Violin plots depict minima and maxima expression levels (14 clusters; n = 8,701 cells from spinal cord of 2 healthy and 2 EAE mice). Genes shown were not differentially expressed. Actb is shown as a reference gene. g, Heat map of top 5 DEGs per single cell cluster. The clusters are ordered by unsupervised hierarchical clustering. Key indicates scaled z-score expression.
