The study introduces CITE-seq, a method that combines single-cell transcriptomics with simultaneous protein detection using DNA-barcoded antibodies. This approach allows for the unbiased and high-throughput analysis of both transcriptomes and epitopes in individual cells. The method integrates antibody-oligo conjugates, which are captured during RNA sequencing, enabling the simultaneous measurement of protein markers and transcriptomes. CITE-seq is compatible with existing single-cell sequencing technologies and can be adapted to various high-throughput applications. The method involves conjugating antibodies to DNA oligonucleotides with unique barcodes, allowing for the identification of specific proteins. Cells are then processed through a microfluidic device to encapsulate them with droplets, where RNA and antibody-derived oligos anneal to beads. This enables the simultaneous sequencing of both mRNA and antibody-derived tags (ADTs). The ADTs are then separated and sequenced alongside the mRNA data, providing a comprehensive view of cellular phenotypes. The study demonstrates the effectiveness of CITE-seq in distinguishing between human and mouse cells based on surface protein expression, as well as in characterizing immune cell subsets. It shows that CITE-seq can provide detailed information on protein expression levels that complement transcriptomic data, enabling more accurate immunophenotyping. The method is validated using flow cytometry and shows high correlation between ADT and RNA-based measurements. CITE-seq also allows for the identification of rare cell populations and the differentiation of immune cell subsets based on protein and RNA expression. The method is scalable and compatible with various single-cell sequencing platforms, making it a valuable tool for studying complex cellular populations. The study highlights the potential of CITE-seq to enhance the understanding of cellular phenotypes by integrating multiple layers of molecular data.The study introduces CITE-seq, a method that combines single-cell transcriptomics with simultaneous protein detection using DNA-barcoded antibodies. This approach allows for the unbiased and high-throughput analysis of both transcriptomes and epitopes in individual cells. The method integrates antibody-oligo conjugates, which are captured during RNA sequencing, enabling the simultaneous measurement of protein markers and transcriptomes. CITE-seq is compatible with existing single-cell sequencing technologies and can be adapted to various high-throughput applications. The method involves conjugating antibodies to DNA oligonucleotides with unique barcodes, allowing for the identification of specific proteins. Cells are then processed through a microfluidic device to encapsulate them with droplets, where RNA and antibody-derived oligos anneal to beads. This enables the simultaneous sequencing of both mRNA and antibody-derived tags (ADTs). The ADTs are then separated and sequenced alongside the mRNA data, providing a comprehensive view of cellular phenotypes. The study demonstrates the effectiveness of CITE-seq in distinguishing between human and mouse cells based on surface protein expression, as well as in characterizing immune cell subsets. It shows that CITE-seq can provide detailed information on protein expression levels that complement transcriptomic data, enabling more accurate immunophenotyping. The method is validated using flow cytometry and shows high correlation between ADT and RNA-based measurements. CITE-seq also allows for the identification of rare cell populations and the differentiation of immune cell subsets based on protein and RNA expression. The method is scalable and compatible with various single-cell sequencing platforms, making it a valuable tool for studying complex cellular populations. The study highlights the potential of CITE-seq to enhance the understanding of cellular phenotypes by integrating multiple layers of molecular data.