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

Nat Methods. 2019 May;16(5):409-412. doi: 10.1038/s41592-019-0392-0. Epub 2019 Apr 22.

Abstract

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • CRISPR-Cas Systems
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Gene Expression Profiling
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Leukocytes, Mononuclear / metabolism
  • Leukocytes, Mononuclear / pathology
  • Lymphoma, T-Cell, Cutaneous / genetics
  • Lymphoma, T-Cell, Cutaneous / metabolism
  • Lymphoma, T-Cell, Cutaneous / pathology
  • Mice
  • NIH 3T3 Cells
  • Proteins / genetics*
  • RNA, Guide / genetics
  • Sequence Analysis, RNA / methods*
  • Single-Cell Analysis / methods*
  • Skin Neoplasms / genetics
  • Skin Neoplasms / metabolism
  • Skin Neoplasms / pathology
  • Transcriptome / genetics*
  • Tumor Cells, Cultured

Substances

  • Proteins
  • RNA, Guide