VATIS UPDATE Article

Scientists at the New York Genome Center (NYGC), the United States, have developed a new technique that represents an important step forward for single-cell RNA sequencing, an advancing field of genomics that provides detailed insights into individual cells and makes it possible to distinguish between different cell types and to study disease mechanisms at the level of individual cells.

Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq), couples the measurement of surface protein markers on thousands of single cells with simultaneous sequencing of the messenger RNA (mRNA or transcriptomes) of those same single cells. The NYGC researchers monitored 10 surface proteins, together with transcriptomes, of 8,000 single cells, the largest scale demonstration of multidimensional single-cell analysis to date.

The protein detection component of CITE-seq is based on DNA-barcoded antibodies, which produce a sequencable readout that is captured along with the transcriptome of the cell. The integration of the protein and RNA data generated by CITE-seq required custom data analysis, was developed in the lab of Rahul Satija, at NYGC. As an example of the power of CITE-seq, the investigators used the multimodal data to identify subclasses of natural killer (NK) cells that are difficult to distinguish based on transcriptomes alone.