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Fig. 1 | Genome Biology

Fig. 1

From: Decontamination of ambient RNA in single-cell RNA-seq with DecontX

Fig. 1

Overview of decontamination with DecontX. a In droplet-based microfluidic devices, ambient RNA can be incorporated into droplets along with oligonucleotide-barcoded beads and cells. Both native mRNA from the cell and contaminating ambient RNA will be barcoded and counted within a droplet. b Left: DecontX assumes that each cell is a mixture of two multinomial distributions: (1) a distribution of native transcripts from the cell’s true population and (2) a distribution of contaminating transcripts from all other cell populations captured in the assay. Right: simulation of an example cell with 20% contamination. The 800 native transcripts are from the multinomial distribution for cell population 1 while the 200 contaminating transcripts are derived from a probability distribution that is a weighted combination of the 2 other populations. c DecontX will take an expression count matrix and cell cluster labels and estimate matrices of native expression and contamination from ambient RNA

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