CITEseq

CITE-seq, short for Cellular Indexing of Transcriptomes and Epitopes by Sequencing, is a single-cell multi-omics method that measures both gene expression and cell-surface protein levels in the same cell. The approach combines antibodies conjugated to DNA oligonucleotide tags with standard single-cell RNA sequencing workflows, enabling parallel profiling of two molecular modalities.

In brief, cells are labeled with antibody-oligo conjugates targeting surface proteins of interest. Each antibody carries a unique DNA tag with a polyA tail. After labeling, cells are processed through a droplet- or well-based single-cell capture system. During lysis, mRNA is captured by polyT on sequencing beads to generate cDNA libraries for the transcriptome, while the antibody-derived tags are captured and amplified separately to form a protein-tag library. Both libraries are sequenced, and reads are mapped to quantify RNA and protein levels in each cell.

CITE-seq is widely used for immune profiling and precise cell type identification, enabling integrated analysis of cellular state at the transcript and protein level. It can improve clustering, lineage inference, and detection of rare populations by complementing RNA data with surface-protein information. The method is compatible with several high-throughput scRNA-seq platforms and data analysis pipelines, with normalization typically applied to ADT data to account for technical variation.

Limitations include dependence on high-quality antibodies, potential non-specific binding, and additional cost and complexity. Antibody panels can influence results, and the method does not measure intracellular proteins without permeabilization. Related approaches include REAP-seq and antibody-derived tag methods, and combinations with sample multiplexing strategies. Overall, CITE-seq provides a robust framework for integrated single-cell multi-omics profiling.