Decontamination of ambient RNA in single-cell RNA-seq with DecontX
Top Cited Papers
Open Access
- 5 March 2020
- journal article
- research article
- Published by Springer Science and Business Media LLC in Genome Biology
- Vol. 21 (1), 1-15
- https://doi.org/10.1186/s13059-020-1950-6
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.Keywords
Funding Information
- National Library of Medicine (R01LM013154-01)
- Informatics Technology for Cancer Research (1U01 CA220413- 01)
This publication has 22 references indexed in Scilit:
- Pharmacokinetics comparison of two pegylated interferon alfa formulations in healthy volunteersBMC Pharmacology and Toxicology, 2018
- Multiplexed droplet single-cell RNA-sequencing using natural genetic variationNature Biotechnology, 2018
- Variational Inference: A Review for StatisticiansJournal of the American Statistical Association, 2017
- Comparative Analysis of Single-Cell RNA Sequencing MethodsMolecular Cell, 2017
- Massively parallel digital transcriptional profiling of single cellsNature Communications, 2017
- Single-cell barcoding and sequencing using droplet microfluidicsNature Protocols, 2016
- Defining cell types and states with single-cell genomicsGenome Research, 2015
- Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter DropletsCell, 2015
- Advances and Applications of Single-Cell Sequencing TechnologiesMolecular Cell, 2015
- The unconventional lifestyle of NKT cellsNature Reviews Immunology, 2002