Extended Data Fig. 4: Single-cell RNA-seq clustering and quality control. | Nature Immunology

Extended Data Fig. 4: Single-cell RNA-seq clustering and quality control.

From: Lupus autoantibodies initiate neuroinflammation sustained by continuous HMGB1:RAGE signaling and reversed by increased LAIR-1 expression

Extended Data Fig. 4

a) UMAP plot colored by clustering. b) UMAP plot split by mouse of origin, colored by cell type. No evidence of strong batch effects in the UMAP space. c) Violin plot of various QC metrics of interest, with similar distributions observed in each mouse. QC metrics include the score returned by Azimuth (Azimuth Score), number of genes per cell (nGene), number of UMI per cell (nUMI), percent UMI coming from mitochondrial reads (Percent Mitochondrial), percent UMI mapping to ribosomal proteins (Percent Ribosomal Protein), and doublet scores (scds). d) Feature plots of genes associated with a known microglia activation signature73. Subclustering within microglia subtypes is largely driven by these variables. e) Feature plots of number of genes per cell (nGene) and number of UMIs per cell (nUMI). Subclustering within microglia subtypes is largely driven by these variables.

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