Extended Data Fig. 8: Nanostring® Glial Profiling Panel was used to validate lowly abundant transcripts discovered using single cell RNASeq experiments.
From: Neuroinflammatory astrocyte subtypes in the mouse brain
a, Schematic for Nanostring Glial Profile Panel experiments. Brain sections from P30 Aldh1l1eGFP mice injected with saline or lipopolysaccharide (LPS) were collected at 3, 24, or 72 h. b, Principle Component (PC) plot of all samples. c, Heatmap of expression level z-scores for 720 genes included in Panel across time since LPS injection. d, Heatmap of z-scores of differentially expressed genes following LPS injection. e, PC plot of genes identified from single cell RNA sequencing (scRNASeq) experiments and enriched in Cluster 8. f, Heatmap of Cluster 8 enriched transcripts. g, Fold-change in expression of Cluster 8 enriched genes with time following LPS injection (compared to the previous time point). h-l, Bar plots showing raw expression values (normalized to chip control transcripts) for individual genes enriched in Cluster 8 (error bars are SEM). While many genes are enriched by 3 h and have lowered expression levels by 24 h, for example Igtp (h), Iigp1 (i), others maintain increased expression for several days (j-l).n = 5 animals per condition. m, PC plot of genes identified from scRNASeq experiments and enriched in Cluster 4. n, Heatmap of Cluster 4 enriched transcripts. N = 5 biological replicates per group. o, Fold-change in expression of Cluster 4 enriched genes with time following LPS injection (compared to the previous time point). p-s, Bar plots showing raw expression values (normalized to Nanostring chip control transcripts) for individual genes enriched in Cluster 4 (error bars are SEM). Abbreviations: LPS, lipopolysaccharide; PC, principle component; QC, quality control (bioAnalyzer chip); scRNASeq, single cell RNA sequencing = 5 biological replicates per group. Prediction ellipses in b,e,m represent probability = 0.95.
