期刊
GENOME BIOLOGY
卷 21, 期 1, 页码 -出版社
BMC
DOI: 10.1186/s13059-020-1950-6
关键词
Bayesian mixture model; Decontamination; Single cell; scRNA-seq
资金
- National Library of Medicine (NLM) [R01LM013154-01]
- Informatics Technology for Cancer Research (ITCR) [1U01 CA220413-01]
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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