Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro.

ABSTRACT: Assays such as CITE-seq can measure the abundance of cell surface proteins on individual cells using antibody derived tags (ADTs). However, many ADTs have high levels of background noise that can obfuscate down-stream analyses. In an exploratory analysis of PBMC datasets, we find that some droplets that were originally called 'empty' due to low levels of RNA contained high levels of ADTs and likely corresponded to neutrophils. We identified a novel type of artifact in the empty droplets called a 'spongelet' which has medium levels of ADT expression and is distinct from ambient noise. ADT expression levels in the spongelets correlate to ADT expression levels in the background peak of true cells in several datasets suggesting that they can contribute to background noise along with ambient AD

SUBMITTER: Yin Y 

PROVIDER: S-EPMC10783508 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature