Decontamination of ambient RNA in single-cell RNA-seq with DecontX.

> 商业许可源文 · EUROPE_PMC · [CC-BY](https://creativecommons.org/licenses/by/)

书目信息

引用：Yang S, Corbett SE, Koga Y, Wang Z, Johnson WE, Yajima M, Campbell JD. (2020). Decontamination of ambient RNA in single-cell RNA-seq with DecontX. Genome biology. PMID 32138770 · PMC7059395 · DOI 10.1186/s13059-020-1950-6

证据类型：PRIMARY_RESEARCH

主题：rna-seq、single-cell

被引次数（采集时）：542

原始记录：[Europe PMC](https://europepmc.org/article/MED/32138770)

来源许可：[CC-BY](https://creativecommons.org/licenses/by/)

作者摘要（按来源许可复用）

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.

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