CITE-seq Protocols v1

This collection contains our main protocols for performing CITE-seq and Cell Hashing, specifically on Drop-seq or10x Genomics single cell 3′ v2 chemistry. CITE-seq: Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) is a multimodal single cell phenotyping method developed in theTechnology Innovation labat the New York Genome Center in collaboration with the Satija lab. CITE-seq uses DNA-barcoded antibodies to convert detection of proteins into a quantitative, sequenceable readout. Antibody-bound oligos act as synthetic transcripts that are captured during most large-scale oligodT-based scRNA-seq library preparation protocols (e.g. 10x Genomics, Drop-seq, ddSeq). This allows for immunophenotyping of cells with a potentially limitless number of markers and unbiased transcriptome analysis using existing single-cell sequencing approaches. Cell Hashing: Sample multiplexing and super-loading onsingle cellRNA-sequencing platforms. Cell Hashinguses a series of oligo-tagged antibodies against ubiquitously expressed surface proteins with different barcodes to uniquely label cells from distinct samples, which can be subsequently pooled in onescRNA-seq run. By sequencing these tags alongside the cellular transcriptome, we can assign each cell to its sample of origin, and robustly identify doublets originating from multiple samples.