Fig. 4. Overview of CITE-seq data processing.

a, Antibody-derived tags (ADTs) are antibody clones with unique barcodes attached to poly(A) sequences and a PCR handle that is specifically amplified in subsequent library processing steps. The antibody binds to surface proteins, and the sequenced ADT counts represent the expression level of those proteins. b, Although ADT data can be unimodally analysed, it is rarely measured alone, but more commonly in conjunction with matching gene expression data. Such paired count matrices of gene expression and ADTs are subject to individual quality control and normalization followed by individual or jointly visualized embeddings. c, The annotation of CITE-seq data can happen at the level of either the transcriptomics data, the ADT data or jointly by matching clusters to both marker gene and marker ADTs. d, To learn about biological mechanisms, ADT data can be tested for differential abundance, cell–cell communication can be inferred and correlation networks of RNA and ADT information can be constructed. q, q value.