Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells

• Published in: Nature methods Vol. 16; no. 5; pp. 409 - 412
• Main Authors: Mimitou, Eleni P., Cheng, Anthony, Montalbano, Antonino, Hao, Stephanie, Stoeckius, Marlon, Legut, Mateusz, Roush, Timothy, Herrera, Alberto, Papalexi, Efthymia, Ouyang, Zhengqing, Satija, Rahul, Sanjana, Neville E., Koralov, Sergei B., Smibert, Peter
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01-05-2019; Nature Publishing Group
• Subjects: 631/1647/2017; 631/250; 631/337; 631/61; Animals; Antigenic determinants; B cells; Bioinformatics; Biological Microscopy; Biological Techniques; Biomedical and Life Sciences; Biomedical Engineering/Biotechnology; Brief Communication; Cell disease research; Cellular proteins; Characterization; Clustered Regularly Interspaced Short Palindromic Repeats; CRISPR; CRISPR-Cas Systems; CRISPR-Cas technology; Epitopes; Gene expression; Gene Expression Profiling; Genetic aspects; Genomes; Genomics; High-Throughput Nucleotide Sequencing - methods; Humans; Identification and classification; Leukocytes, Mononuclear - metabolism; Leukocytes, Mononuclear - pathology; Life Sciences; Lymphoma, T-Cell, Cutaneous - genetics; Lymphoma, T-Cell, Cutaneous - metabolism; Lymphoma, T-Cell, Cutaneous - pathology; Membrane proteins; Methods; Mice; NIH 3T3 Cells; Phenotyping; Proteins; Proteins - genetics; Proteomics; Ribonucleic acid; RNA; RNA sequencing; RNA, Guide, CRISPR-Cas Systems - genetics; Screens; Sequence Analysis, RNA - methods; Single-Cell Analysis - methods; Skin Neoplasms - genetics; Skin Neoplasms - metabolism; Skin Neoplasms - pathology; Technological innovations; Technology; Transcriptome - genetics; Tumor Cells, Cultured; United States
• ISSN: 1548-7091; 1548-7105
• DOI: 10.1038/s41592-019-0392-0

Multimodal single-cell assays provide high-resolution snapshots of complex cell populations, but are mostly limited to transcriptome plus an additional modality. Here, we describe expanded CRISPR-compatible cellular indexing of transcriptomes and epitopes by sequencing (ECCITE-seq) for the high-throughput characterization of at least five modalities of information from each single cell. We demonstrate application of ECCITE-seq to multimodal CRISPR screens with robust direct single-guide RNA capture and to clonotype-aware multimodal phenotyping of cancer samples.
ECCITE-seq combines the single-cell analysis of multiple modalities, for example transcriptome, immune cell receptors, cell surface proteins and single-guide RNAs.