Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets

Evan Z. Macosko, Anindita Basu, Rahul Satija, James Nemesh, Karthik Shekhar, Melissa Goldman, Itay Tirosh, Allison R. Bialas, Nolan Kamitaki, Emily M. Martersteck, John J. Trombetta, David A. Weitz, Joshua R. Sanes, Alex K. Shalek, Aviv Regev, Steven A. McCarroll

Research output: Contribution to journalArticle

Abstract

Cells, the basic units of biological structure and function, vary broadly in type and state. Single-cell genomics can characterize cell identity and function, but limitations of ease and scale have prevented its broad application. Here we describe Drop-seq, a strategy for quickly profiling thousands of individual cells by separating them into nanoliter-sized aqueous droplets, associating a different barcode with each cell's RNAs, and sequencing them all together. Drop-seq analyzes mRNA transcripts from thousands of individual cells simultaneously while remembering transcripts' cell of origin. We analyzed transcriptomes from 44,808 mouse retinal cells and identified 39 transcriptionally distinct cell populations, creating a molecular atlas of gene expression for known retinal cell classes and novel candidate cell subtypes. Drop-seq will accelerate biological discovery by enabling routine transcriptional profiling at single-cell resolution. Video Abstract

Original languageEnglish (US)
Pages (from-to)1202-1214
Number of pages13
JournalCell
Volume161
Issue number5
DOIs
StatePublished - May 30 2015

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Genes
Genome
Cells
Gene expression
RNA
Messenger RNA
RNA Sequence Analysis
Atlases
Genomics
Transcriptome
Gene Expression

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., ... McCarroll, S. A. (2015). Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell, 161(5), 1202-1214. https://doi.org/10.1016/j.cell.2015.05.002

Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. / Macosko, Evan Z.; Basu, Anindita; Satija, Rahul; Nemesh, James; Shekhar, Karthik; Goldman, Melissa; Tirosh, Itay; Bialas, Allison R.; Kamitaki, Nolan; Martersteck, Emily M.; Trombetta, John J.; Weitz, David A.; Sanes, Joshua R.; Shalek, Alex K.; Regev, Aviv; McCarroll, Steven A.

In: Cell, Vol. 161, No. 5, 30.05.2015, p. 1202-1214.

Research output: Contribution to journalArticle

Macosko, EZ, Basu, A, Satija, R, Nemesh, J, Shekhar, K, Goldman, M, Tirosh, I, Bialas, AR, Kamitaki, N, Martersteck, EM, Trombetta, JJ, Weitz, DA, Sanes, JR, Shalek, AK, Regev, A & McCarroll, SA 2015, 'Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets', Cell, vol. 161, no. 5, pp. 1202-1214. https://doi.org/10.1016/j.cell.2015.05.002
Macosko, Evan Z. ; Basu, Anindita ; Satija, Rahul ; Nemesh, James ; Shekhar, Karthik ; Goldman, Melissa ; Tirosh, Itay ; Bialas, Allison R. ; Kamitaki, Nolan ; Martersteck, Emily M. ; Trombetta, John J. ; Weitz, David A. ; Sanes, Joshua R. ; Shalek, Alex K. ; Regev, Aviv ; McCarroll, Steven A. / Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. In: Cell. 2015 ; Vol. 161, No. 5. pp. 1202-1214.
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