Droplet-based microfluidic devices have become widely used to perform single-cell RNA sequencing (scRNA-seq). However, ambient RNA present in the cell suspension can be aberrantly counted along with a cell’s native mRNA and result in cross-contamination of transcripts between different cell populations. DecontX is a novel Bayesian method to estimate and remove contamination in individual cells. DecontX accurately predicts contamination levels in a mouse-human mixture dataset and removes aberrant expression of marker genes in PBMC datasets. We also compare the contamination levels between four different scRNA-seq protocols. Overall, DecontX can be incorporated into scRNA-seq workflows to improve downstream analyses.

中文翻译：

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使用 DeconX 在单细胞 RNA-seq 中净化环境 RNA

基于液滴的微流体装置已被广泛用于执行单细胞 RNA 测序 (scRNA-seq)。然而，存在于细胞悬液中的环境 RNA 可能会与细胞的天然 mRNA 一起被异常计数，并导致不同细胞群之间转录物的交叉污染。DeconX 是一种新颖的贝叶斯方法，用于估计和去除单个细胞中的污染。DeconX 准确预测小鼠-人类混合数据集中的污染水平，并去除 PBMC 数据集中标记基因的异常表达。我们还比较了四种不同 scRNA-seq 协议之间的污染水平。总的来说，DecontX 可以整合到 scRNA-seq 工作流程中以改进下游分析。