Extended Data Fig. 1: scRNA-seq demultiplexing and quality assessment. | Nature Medicine

Extended Data Fig. 1: scRNA-seq demultiplexing and quality assessment.

From: An immune-cell signature of bacterial sepsis

Extended Data Fig. 1

(a) Sample strategy for gating for hashtag oligo (HTO) positive cells based on UMI tag counts of each barcode. (b) Histogram of cells per 10X gel beads in emulsion (GEM) barcode for one representative channel. Data are shown for one channel with n = 15,304 detected GEMs. (c) tSNE plots of all cells (n = 126,351 cells total from 65 individuals) in the study colored by institution of origin of the cohort, hashtag barcode, and processing batch. Adjusted Rand index is shown for each when compared with cell state assignments. (d) Violin plots (n = 126,351 cells total from 65 individuals) of various quality control metrics for the full scRNA-seq dataset generated in this study. (e) Violin plots of genes detected across different cell-types (n = 32,341, 7,970, 9,390, 58,557, 14,299, 3,794 cells for T, B, NK, Mono, DC, and MK, respectively). Violin plots show a kernel density estimate of the data, using Scott’s rule to calculate the appropriate kernel bandwidth. The violin extends to 2x the bandwidth in both directions.

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