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Glioblastoma pp 151-170 | Cite as

Single-Cell RNA Sequencing of Glioblastoma Cells

  • Rajeev Sen
  • Igor Dolgalev
  • N. Sumru Bayin
  • Adriana Heguy
  • Aris Tsirigos
  • Dimitris G. PlacantonakisEmail author
Protocol
Part of the Methods in Molecular Biology book series (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.

Keywords

RNA sequencing Single cell RNASeq Transcriptome Bioinformatics Fluidigm Seurat 

Notes

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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Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  • Rajeev Sen
    • 1
  • Igor Dolgalev
    • 2
    • 3
  • N. Sumru Bayin
    • 1
    • 4
  • Adriana Heguy
    • 5
  • Aris Tsirigos
    • 2
    • 3
  • Dimitris G. Placantonakis
    • 1
    • 4
    • 6
    • 7
    • 8
    Email author
  1. 1.Department of NeurosurgeryNew York University School of MedicineNew YorkUSA
  2. 2.Department of PathologyNew York University School of MedicineNew YorkUSA
  3. 3.Applied Bioinformatics CenterNew York University School of MedicineNew YorkUSA
  4. 4.Kimmel Center for Stem Cell BiologyNew York University School of MedicineNew YorkUSA
  5. 5.Genome Technology CenterNew York University School of MedicineNew YorkUSA
  6. 6.Perlmutter Cancer CenterNew York University School of MedicineNew YorkUSA
  7. 7.Brain Tumor CenterNew York University School of MedicineNew YorkUSA
  8. 8.Neuroscience InstituteNew York University School of MedicineNew YorkUSA

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