Credit: Yuan Yin et al.
Boston University researchers have developed a novel method to rectify the issue of high background noise when using CITE-seq. By identifying and removing numerous types of contaminants, the tool could improve the data quality of CITE-seq workflows.
CITE-seq (cellular indexing of transcriptomes and epitopes), is often used to quantify cell surface protein and transcriptomic data within a single cell readout. While CITE-seq offers researchers a method of detecting a limited number of proteins during single-cell sequencing, its high background noise can hinder the analysis. To solve this problem, researchers from Boston University developed a tool that can identify and remove most of this background noise.
The tool, published in Nucleic Acids Research, is called DecontPro and is effective at identifying and reducing background noise from numerous sources. “We created DecontPro, a statistical model that decontaminates two sources of contamination that were observed empirically in CITE-seq data,” said Joshua Campbell, associate professor of medicine at Boston University. “It can be used as an important quality assessment tool that will aid in the downstream analysis and help researchers to better understand the molecular cause of disease.”
While developing DecontPro, the researchers discovered a common artifact they called a “spongelet.” In several datasets examined, these spongelets caused a significant amount of the background noise that was observed. Further testing showed that DecontPro was effective at estimating and removing the background noise from these spongelets along with other contaminants.
“DecontPro is a Bayesian hierarchical model. We carefully constructed it so that it can tease apart the signals from noise in single-cell datasets without being overly aggressive,” said Masanao Yajima, professor in the department of mathematics and statistics at Boston University.
The researchers believe that DecontPro outperforms other tools and its integration into CITE-seq workflows could improve downstream analysis quality.