Key Considerations on CITE-Seq for Single-Cell Multiomics

CITE-Seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) is an advanced single-cell sequencing method to profile both gene expression and protein abundance simultaneously in individual cells using single-cell mRNA sequencing techniques alongside antibody-derived tags (ADTs), for protein detection. The characterization of both the transcriptome and the proteome from the same cells provides a powerful and multiomic approach for understanding the mechanisms of complex biological processes. This review focuses on the workflow of CITE-Seq using a microwell-based single-cell analysis system as an example and provides key considerations for staining cells with ADTs. By highlighting critical information for CITE-Seq library preparation, sequencing, and data analysis, this review provides a practical guide with which to perform comprehensive CITE-Seq workflow.