Figure 1:
ECCITE-seq allows simultaneous detection of transcriptome, proteins, clonotypes and CRISPR perturbations. a. Schematic overview of the multiple cellular modalities captured by ECCITE-seq. cDNAs derived from mRNA and sgRNA transcripts acquire cell barcodes and unique identifiers through a template switch reaction with the bead-bound oligo, whereas protein tags harbor sequences that allow direct annealing to the bead oligo. Reverse transcription and amplification yields products with distinct sizes that can be separated and amplified independently (right panel). b. Species-mixing experiment. Left: number of transcripts associated with each cell barcode (red, >90% human reads; green, >90% mouse reads; blue, >10% human and mouse (multiplet). Right: sgRNA reads associated with each cell barcode. Points are colored based on species classifications using transcripts. c. Transcriptome-based clustering of single-cell expression profiles of the mixed human and mouse sample, illustrating the 5 modalities of ECCITE-seq: Transcriptome, Cell Hashing [I], Protein [II], T cell antigen receptors (α/β: red, γ/δ: blue) [III] and sgRNAs [IV]. d. Number of cell barcodesbefore (purple) or after (blue) removal of cell doublets assigned zero, one or two unique guides per cell in two independent experiments and cell lines. e. K562 cells were clustered based on normalized and scaled sgRNA counts. Highlighted are counts for sgRNAs (black) targeting the indicated gene and counts for respective mRNA (blue) and protein tags (green) where applicable.