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      Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

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          Abstract

          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. VIDEO ABSTRACT.

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          Author and article information

          Journal
          Cell
          Cell
          Elsevier BV
          00928674
          May 2015
          May 2015
          : 161
          : 5
          : 1187-1201
          Article
          10.1016/j.cell.2015.04.044
          26000487
          4c646204-d949-48fe-ae17-3eb01c9d1eba
          © 2015

          https://www.elsevier.com/tdm/userlicense/1.0/

          https://www.elsevier.com/open-access/userlicense/1.0/

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