Single-Cell Library Preparation of iPSC-Derived Neural Stem Cells

  • Jeffrey Kim
  • Marcel M. DaadiEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1919)


Single-cell RNA-seq technology allows for the identification of heterogeneous cell populations, measures stochastic gene expressions, and identifies highly variable genes. Thus, with this technology it is possible to identify relevant pathways involved in development or in disease progression. Herein, we describe a protocol to capture and process single-cell transcriptomes that will be used for RNA sequencing. This chapter discusses the use of the Fluidigm C1 System and Integrated Fluidic Circuit microfluidics system, TapeStation 4200, SMART-Seq v4, Nextera XT Library Preparation Kit, and AMPure XP beads.

Key words

Single cell Neural stem cells Fluidigm C1 Library preparation RNA-seq Single-cell RNA-seq Nextera XT Next-generation sequencing SMART-Seq 



The authors thank members of the Daadi laboratory for the helpful support and suggestions. This work was supported by the Worth Family Fund, the Perry & Ruby Stevens Charitable Foundation and the Robert J., Jr. and Helen C. Kleberg Foundation, the NIH primate center base grant (Office of Research Infrastructure Programs/OD P51 OD011133), and the National Center for Advancing Translational Sciences, National Institutes of Health, through Grant UL1 TR001120.

Disclosures: Dr. Marcel M. Daadi is founder of the biotech company NeoNeuron.


  1. 1.
    Behjati S, Tarpey PS (2013) What is next generation sequencing? Arch Dis Child Educ Pract Ed 98:236–238CrossRefGoogle Scholar
  2. 2.
    Bengtsson M, Ståhlberg A, Rorsman P, Kubista M (2005) Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels. Genome Res 15:1388–1392CrossRefGoogle Scholar
  3. 3.
    Islam S et al (2011) Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res 21:1160–1167CrossRefGoogle Scholar
  4. 4.
    Gross A et al (2015) Technologies for single-cell isolation. Int J Mol Sci 16:16897–16919CrossRefGoogle Scholar
  5. 5.
    Welzel G, Seitz D, Schuster S (2015) Magnetic-activated cell sorting (MACS) can be used as a large-scale method for establishing zebrafish neuronal cell cultures. Sci Rep 5:7959CrossRefGoogle Scholar
  6. 6.
    Datta S et al (2015) Laser capture microdissection: big data from small samples. Histol Histopathol 30:1255–1269PubMedPubMedCentralGoogle Scholar
  7. 7.
    Bhagat AAS et al (2010) Microfluidics for cell separation. Med Biol Eng Comput 48:999–1014CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Southwest National Primate Research CenterTexas Biomedical Research InstituteSan AntonioUSA
  2. 2.Department of Radiology, Research Imaging Institute, Cell Systems and Anatomy, Long School of MedicineUniversity of Texas Health Science Center at San Antonio San AntonioUSA

Personalised recommendations