Figure 1. CITE-seq enables simultaneous detection of single cell transcriptomes and protein markers.
(a) Illustration of the DNA-barcoded antibodies used in CITE-seq. (b) Schematic representation of CITE-seq in combination with Drop-seq1. Cells are incubated with antibodies, washed and passed through a microfluidic chip where a single cell and one bead are occasionally encapsulated in the same droplet. After cell lysis mRNAs and antibody-oligos anneal to oligos on Drop-seq beads, linking cell barcodes with cellular transcripts and antibody-derived oligos. (c – e) Analysis of mixtures of mouse and human cells that were incubated with oligo-tagged-antibodies specific for either human or mouse cell-surface markers (integrin beta CD29) and processed by Drop-seq. (c) Quantification of the number of human and mouse transcripts associating to each cell barcode. Green: >90% human reads, Red: >90% mouse reads, Blue: >10% human and mouse (multiplet). (d) Quantification of antibody tags (ADTs) associated with each cell barcode. Points are colored based on species classifications using transcripts in (c). (e) Quantification of human, mouse or mixed-cell barcodes based on RNA transcripts, or ADTs.