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Characterization of directed differentiation by high-throughput single-cell RNA-Seq

Magali Soumillon, Davide Cacchiarelli, Stefan Semrau, Alexander van Oudenaarden, Tarjei S. Mikkelsen
doi: https://doi.org/10.1101/003236
Magali Soumillon
1Broad Institute, Cambridge, Massachusetts 02142, USA
2Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
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Davide Cacchiarelli
1Broad Institute, Cambridge, Massachusetts 02142, USA
2Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
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Stefan Semrau
3Departments of Physics and Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
4Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
5Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
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Alexander van Oudenaarden
5Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
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Tarjei S. Mikkelsen
1Broad Institute, Cambridge, Massachusetts 02142, USA
2Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
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  • For correspondence: tarjei@broadinstitute.org
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Abstract

Directed differentiation of cells in vitro is a powerful approach for dissection of developmental pathways, disease modeling and regenerative medicine, but analysis of such systems is complicated by heterogeneous and asynchronous cellular responses to differentiation-inducing stimuli. To enable deep characterization of heterogeneous cell populations, we developed an efficient digital gene expression profiling protocol that enables surveying of mRNA in thousands of single cells at a time. We then applied this protocol to profile 12,832 cells collected at multiple time points during directed adipogenic differentiation of human adipose-derived stem/stromal cells in vitro. The resulting data reveal the major axes of cell-to-cell variation within and between time points, and an inverse relationship between inflammatory gene expression and lipid accumulation across cells from a single donor.

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Posted March 05, 2014.
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Characterization of directed differentiation by high-throughput single-cell RNA-Seq
Magali Soumillon, Davide Cacchiarelli, Stefan Semrau, Alexander van Oudenaarden, Tarjei S. Mikkelsen
bioRxiv 003236; doi: https://doi.org/10.1101/003236
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Characterization of directed differentiation by high-throughput single-cell RNA-Seq
Magali Soumillon, Davide Cacchiarelli, Stefan Semrau, Alexander van Oudenaarden, Tarjei S. Mikkelsen
bioRxiv 003236; doi: https://doi.org/10.1101/003236

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