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Single-Cell RNA Sequencing of Glioblastoma Cells

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Glioblastoma

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1741))

Abstract

Single-cell RNA sequencing (sc-RNASeq) is a recently developed technique used to evaluate the transcriptome of individual cells. As opposed to conventional RNASeq in which entire populations are sequenced in bulk, sc-RNASeq can be beneficial when trying to better understand gene expression patterns in markedly heterogeneous populations of cells or when trying to identify transcriptional signatures of rare cells that may be underrepresented when using conventional bulk RNASeq. In this method, we describe the generation and analysis of cDNA libraries from single patient-derived glioblastoma cells using the C1 Fluidigm system. The protocol details the use of the C1 integrated fluidics circuit (IFC) for capturing, imaging and lysing cells; performing reverse transcription; and generating cDNA libraries that are ready for sequencing and analysis.

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Acknowledgments

We would like to thank Fluidigm for sharing schematic images on using the C1 System, and Yutong Zhang from the NYU Langone Genome Technology Center for expert technical assistance.

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Authors and Affiliations

  1. Department of Neurosurgery, New York University School of Medicine, New York, NY, USA

    Rajeev Sen, N. Sumru Bayin & Dimitris G. Placantonakis

  2. Department of Pathology, New York University School of Medicine, New York, NY, USA

    Igor Dolgalev & Aris Tsirigos

  3. Applied Bioinformatics Center, New York University School of Medicine, New York, NY, USA

    Igor Dolgalev & Aris Tsirigos

  4. Kimmel Center for Stem Cell Biology, New York University School of Medicine, New York, NY, USA

    N. Sumru Bayin & Dimitris G. Placantonakis

  5. Genome Technology Center, New York University School of Medicine, New York, NY, USA

    Adriana Heguy

  6. Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA

    Dimitris G. Placantonakis

  7. Brain Tumor Center, New York University School of Medicine, New York, NY, USA

    Dimitris G. Placantonakis

  8. Neuroscience Institute, New York University School of Medicine, New York, NY, USA

    Dimitris G. Placantonakis

Authors
  1. Rajeev Sen
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  2. Igor Dolgalev
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  3. N. Sumru Bayin
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  4. Adriana Heguy
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  5. Aris Tsirigos
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  6. Dimitris G. Placantonakis
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Corresponding author

Correspondence to Dimitris G. Placantonakis .

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Editors and Affiliations

  1. Department of Neurosurgery, NYU School of Medicine, New York, New York, USA

    Dimitris G. Placantonakis

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Sen, R., Dolgalev, I., Bayin, N.S., Heguy, A., Tsirigos, A., Placantonakis, D.G. (2018). Single-Cell RNA Sequencing of Glioblastoma Cells. In: Placantonakis, D. (eds) Glioblastoma. Methods in Molecular Biology, vol 1741. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7659-1_12

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  • DOI: https://doi.org/10.1007/978-1-4939-7659-1_12

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7658-4

  • Online ISBN: 978-1-4939-7659-1

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