Cell
Volume 161, Issue 5, 21 May 2015, Pages 1202-1214
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Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

https://doi.org/10.1016/j.cell.2015.05.002Get rights and content
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Highlights

  • Drop-seq enables highly parallel analysis of individual cells by RNA-seq

  • Drop-seq encapsulates cells in nanoliter droplets together with DNA-barcoded beads

  • Systematic evaluation of Drop-seq library quality using species mixing experiments

  • Drop-seq analysis of 44,808 cells identifies 39 cell populations in the retina

Summary

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.

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