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

Eleni P. Mimitou, Anthony Cheng, Antonino Montalbano, Stephanie Hao, Marlon Stoeckius, Mateusz Legut, Timothy Roush, Alberto Herrera, Efthymia Papalexi, Zhengqing Ouyang, Rahul Satija, Neville E. Sanjana, Sergei B. Koralov, Peter Smibert

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)409-412
Number of pages4
JournalNature Methods
Volume16
Issue number5
DOIs
StatePublished - May 1 2019

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Clustered Regularly Interspaced Short Palindromic Repeats
Transcriptome
Epitopes
Guide RNA
Proteins
Assays
Cells
Throughput
Population
Neoplasms

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Mimitou, E. P., Cheng, A., Montalbano, A., Hao, S., Stoeckius, M., Legut, M., ... Smibert, P. (2019). Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells. Nature Methods, 16(5), 409-412. https://doi.org/10.1038/s41592-019-0392-0

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

In: Nature Methods, Vol. 16, No. 5, 01.05.2019, p. 409-412.

Research output: Contribution to journalArticle

Mimitou, EP, Cheng, A, Montalbano, A, Hao, S, Stoeckius, M, Legut, M, Roush, T, Herrera, A, Papalexi, E, Ouyang, Z, Satija, R, Sanjana, NE, Koralov, SB & Smibert, P 2019, 'Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells', Nature Methods, vol. 16, no. 5, pp. 409-412. https://doi.org/10.1038/s41592-019-0392-0
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. / Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells. In: Nature Methods. 2019 ; Vol. 16, No. 5. pp. 409-412.
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