mRNA sequencing of clinical-grade neural stem cells derived from human ES cells

We report the transcriptome profile of human neural stem cells derived from ES cells. Cells were transplanted into rodent models, and mRNA transcripts from the chimeric graft tissue were bioinformatically split according to species of origin. Overall design: Human (h)ES lines H9 and ESI-017 were differentiated into neural stem/progenitor cells (NSCs/NPCs) using a clonal morphology basis of selection, as described in Bohaciakova et al., 2019. Expression (RNA-seq) analysis of these clonal morphology (CoMo)-derived NSC suspensions demonstrate similar gene expression profiles to NSCs that were purified with FACs methods. We injected independently H9- and ESI-017-derived NSC suspensions in the central grey matter of the spinal lumbar region of n=10 adult rats (Rat 1-4, and Rat 5-10, respectively). After 1 week, 1, 2, or 8 months in H9 hESC-NSC-injected rats (Rat 1-4, respectively), and 2 or 6 months in ESI-017 hESC-NSC-injected rats (Rat 5-7 and Rat 8-10, respectively), grafted cells were processed for RNA-seq analysis. We used these samples to profile the patterns of cPcdh variations, as described in Almenar-Queralt et al., 2019. Human and rat reads were separated according to species (HG and RN) by bioinformatics methods.