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