This webinar describes a protocol and proof-of-principle experiments for Cellular Indexing of Transcriptome and Epitopes by Sequencing (CITE-seq).

CITE-seq combines unbiased genome-wide expression profiling with the measurement of a potentially limitless number of specific protein markers in thousands of single cells.

Marlon Stoeckius, Research Scientist in the Technology Innovation Lab of the New York Genome Center, presents the approach, which first requires conjugating monoclonal antibodies to oligonucleotides containing unique antibody identifier sequences. Next, a cell suspension is labeled with the DNA-barcoded antibodies and single cells are subsequently encapsulated into nanoliter-sized aqueous droplets in a microfluidic apparatus. In each droplet, cells are lysed, antibody and cDNA molecules are indexed with the same unique barcode, and the resulting molecules are converted into libraries. The protein-encoding and RNA-derived libraries can be amplified independently and mixed in appropriate proportions for sequencing in the same lane.

Dr. Stoeckius discusses proof-of-concept experiments, highlight the method’s compatibility with existing single-cell sequencing approaches, and describes how it can readily scale as the throughput of these methods increases.