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Fig. 1 | Genome Biology

Fig. 1

From: Single-cell RNA-seq with spike-in cells enables accurate quantification of cell-specific drug effects in pancreatic islets

Fig. 1

Spike-ins enable assessment of contamination in scRNA-seq experiments. a Islet treatment and sample preparation scheme. b Expression (log TPM) of insulin and glucagon in all cells of DMSO-treated islets from human donors I and II. Horizontal lines indicate the shifts of the non-alpha and non-beta cells from non-expressing levels. Red dotted line: baseline expression for non-islet cells as reported in the Human Cell Atlas (HCA). c Expression of insulin and glucagon in external datasets. TPM and RPKM values reported in each dataset were log transformed. d Alignment of reads to both the human and mouse genomes to identify spike-in reference cells, here mouse spike-ins in a human sample (DMSO, donor II). e Contamination of mouse spike-ins in human samples. Contamination is quantified as the percentage of reads aligned to the human genome in mouse spike-ins. f Correlation of the contamination profile within the mouse spike-in cells in human samples. g Average contamination in mouse spike-ins (y-axis) versus average expression in the sample (human pancreatic cells, x-axis) shown for sample DMSO, human donor II. Spearman correlation R = 0.888. h Average expression (log TPM) of genes with the largest difference in mouse and human spike-ins, and external references

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