The paper introduces CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing), a method that integrates protein and transcriptome measurements in single cells using oligonucleotide-labeled antibodies. This approach combines highly multiplexed antibody-based detection of protein markers with unbiased transcriptome profiling, enabling detailed characterization of cellular phenotypes. CITE-seq is adaptable to existing high-throughput single-cell RNA sequencing methods and can achieve more precise immunophenotyping compared to single-cell RNA sequencing (scRNA-seq) alone. The method is validated through experiments with immune cells, demonstrating its ability to distinguish cell types based on surface protein expression and to resolve subpopulations within clusters. CITE-seq provides a multimodal readout that complements scRNA-seq, offering a more comprehensive understanding of cellular states and functions.The paper introduces CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing), a method that integrates protein and transcriptome measurements in single cells using oligonucleotide-labeled antibodies. This approach combines highly multiplexed antibody-based detection of protein markers with unbiased transcriptome profiling, enabling detailed characterization of cellular phenotypes. CITE-seq is adaptable to existing high-throughput single-cell RNA sequencing methods and can achieve more precise immunophenotyping compared to single-cell RNA sequencing (scRNA-seq) alone. The method is validated through experiments with immune cells, demonstrating its ability to distinguish cell types based on surface protein expression and to resolve subpopulations within clusters. CITE-seq provides a multimodal readout that complements scRNA-seq, offering a more comprehensive understanding of cellular states and functions.