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

Genome Biology
Shiyi YangJoshua D. Campbell

Abstract

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.

References

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Citations

Jul 6, 2020·European Respiratory Review : an Official Journal of the European Respiratory Society·Michael J AlexanderPaul A Reyfman
May 27, 2020·Nature Microbiology·Sydney B BlattmanSaeed Tavazoie
Jan 15, 2021·Arteriosclerosis, Thrombosis, and Vascular Biology·Jean AcostaPeter van Galen
Feb 17, 2021·Nature Methods·Adam GayosoNir Yosef
Mar 9, 2021·Parasitology·Emma M BriggsThomas D Otto
May 25, 2021·JHEP Reports : Innovation in Hepatology·Valéry L PayenAdil El Taghdouini
Aug 13, 2021·Journal of Neurogenetics·Aaron M Allen, Marla B Sokolowski
Jul 20, 2021·Physiological Reviews·Adam Ramzy, Timothy J Kieffer

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Methods Mentioned

BETA
scRNA-seq
flow cytometry
CEL-seq2
Drop-seq
PCA

Software Mentioned

demuxlet
DecontX
tSNE
DBSCAN
Scrublet
scds
Celda
UMAP
DoubletFinder
CellRanger

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