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
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Research Support, N.I.H., Extramural
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Research Support, Non-U.S. Gov't
MeSH terms
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Animals
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CRISPR-Cas Systems
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Clustered Regularly Interspaced Short Palindromic Repeats
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Gene Expression Profiling
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High-Throughput Nucleotide Sequencing / methods*
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Humans
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Leukocytes, Mononuclear / metabolism
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Leukocytes, Mononuclear / pathology
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Lymphoma, T-Cell, Cutaneous / genetics
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Lymphoma, T-Cell, Cutaneous / metabolism
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Lymphoma, T-Cell, Cutaneous / pathology
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Mice
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NIH 3T3 Cells
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Proteins / genetics*
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RNA, Guide, CRISPR-Cas Systems / genetics
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Sequence Analysis, RNA / methods*
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Single-Cell Analysis / methods*
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Skin Neoplasms / genetics
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Skin Neoplasms / metabolism
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Skin Neoplasms / pathology
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Transcriptome / genetics*
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Tumor Cells, Cultured
Substances
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Proteins
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RNA, Guide, CRISPR-Cas Systems