Extended Data Fig. 1: Quality control for 10x Genomics single-cell RNA-seq data.
From: Single-cell analysis reveals T cell infiltration in old neurogenic niches
a, Unique gene counts for 14,685 cells, separated by cell type and individual mouse (complete cell count breakdown available in Supplementary Table 3). Mean ± 25th and 75th percentile are shown by central and outer lines of the boxes; upper and lower whiskers extend to 1.5× of the interquartile range. b, Heat map showing the expression of the top five marker genes for each significant cell cluster identified by Seurat. The cell identity assigned to each cluster is indicated on the bottom of each column. c, t-SNE plots of all 14,685 single-cell transcriptomes analysed by the 10x Genomics platform, coloured by replicates (left), individual mouse (centre), and separated by age (two right-hand plots). Clustering was the same as for Fig. 1a. Eight thousand eight hundred and eighty-four cells from young (young 1, 2,306; young 2, 2,675; young 3, 3,903) and 5,801 cells from old (old 1, 1,435; old 2, 2,541; old 3, 1,825).
