title: Illumina NovaSeq 6000 paired end sequencing; Epigenetic profile of iPSC differentiation process by scRNA-seq
design: Epigenetic profile of iPSC differentiation process by scRNA-seq
library_construction_protocol: Dermal fibroblasts obtained from skin biopsies of two different healthy subjects (A and B) were cultured in fibroblast medium and reprogrammed with the Sendai virus technology (CytoTune-iPS Sendai Reprogramming Kit, ThermoFisher, Waltham, MA, USA) to generate Human iPSC clones. iPS clones were individually picked, expanded and maintained in mTeSR1 on hESC-qualified Matrigel. Human iPSC-derived NPC were generated following the standard protocol based on a dual-smad inhibition (doi: https://doi.org/10.1371/journal.pone.0059252). Briefly, hiPSCs were differentiated in hNPC via human embryoid bodies. Neural induction was initiated through inhibition using the dual-small inhibition molecules dorsomorphin, purmorphamine, and SB43152. The small molecule CHIR99021, a GSK3b inhibitor, was added to stimulate the canonical WNT signaling pathway. Nucleic acids were directly processed on intact cells following standard Chromium Single Cell 3' Reagent v3 chemistry protocol (10X Genomics) using  Chromium platform (10x Genomics). Target cell recovery was 5'000. Libraries were prepared using Chromium Single Cell 3' Reagent v3 chemistry protocol (10X Genomics). Library quality was assessed using TapeStation (Agilent Technologies). Libraries were sequenced on NovaSeq 6000 platform (Illumina) aiming at 50'000 clusters/cell.