Understanding and mitigating the impact of ambient mRNA contamination in single-cell RNA-sequencing analysis.

ABSTRACT: Droplet-based single-cell RNA sequencing (scRNA-seq) frequently encounters significant challenges from contamination of cell-free mRNAs, known as "ambient mRNAs", which can substantially distort single-cell transcriptome data interpretation to a large extent. In this study, we investigate the impact of ambient mRNA contamination on differential gene expression and biological pathway enrichment analyses, using two independent scRNA-seq datasets: ten peripheral blood mononuclear cells (PBMCs) samples from dengue-infected patients and forty-two scRNA-seq samples of human fetal liver tissues. We apply two independent ambient mRNA correction approaches - CellBender (automate correction) and SoupX (using a predefined set of potential ambient mRNA genes). We demonstrate that ambient mRNA transcri

SUBMITTER: Arora JK 

PROVIDER: S-EPMC12459771 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature