Cell
Volume 161, Issue 5, 21 May 2015, Pages 1187-1201
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Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

https://doi.org/10.1016/j.cell.2015.04.044Get rights and content
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Highlights

  • Cells are captured and barcoded in nanolitre droplets with high capture efficiency

  • Each drop hosts a hydrogel carrying photocleavable combinatorially barcoded primers

  • mRNA of thousands of mouse embryonic stem and differentiating cells are sequenced

  • Single-cell heterogeneity reveals population structure and gene regulatory linkages

Summary

It has long been the dream of biologists to map gene expression at the single-cell level. With such data one might track heterogeneous cell sub-populations, and infer regulatory relationships between genes and pathways. Recently, RNA sequencing has achieved single-cell resolution. What is limiting is an effective way to routinely isolate and process large numbers of individual cells for quantitative in-depth sequencing. We have developed a high-throughput droplet-microfluidic approach for barcoding the RNA from thousands of individual cells for subsequent analysis by next-generation sequencing. The method shows a surprisingly low noise profile and is readily adaptable to other sequencing-based assays. We analyzed mouse embryonic stem cells, revealing in detail the population structure and the heterogeneous onset of differentiation after leukemia inhibitory factor (LIF) withdrawal. The reproducibility of these high-throughput single-cell data allowed us to deconstruct cell populations and infer gene expression relationships.

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