Bioinformatics Analysis of Single-Cell RNA-Seq Raw Data from iPSC-Derived Neural Stem Cells

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


This chapter describes a pipeline for basic bioinformatics analysis of single-cell sequencing data (see Chap.  10: Single-Cell Library Preparation). Starting with raw sequencing data, we describe how to quality check samples, to create an index from a reference genome, to align the sequences to an index, and to quantify transcript abundances. The curated data sets will enable differential expression analysis, population analysis, and pathway analysis.

Key words

Single cell Neural stem cells Fluidigm C1 Bioinformatics Single-cell analysis Single-cell RNA-seq RNA-seq Singular SCDE Kallisto Sleuth DAVID BBDuk FASTQC 



The authors thank the members of the Daadi laboratory for their 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.

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 AntonioSan AntonioUSA

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