RNA-seq data analysis

Total RNA extraction from OLIG2::eGFP fibroblasts, human dermal fibroblasts, A2B5⁺ iOPCs (BJ), A2B5⁺ iOPCs (HDFs), O4⁺ iOPCs (BJ, 2D), OLIG2⁺ iOPCs, and SOX10⁺ iOPCs was performed using TRIzol (Thermo Fisher Scientific), and genomic DNA was removed by DNase I. RNA quality was checked with an Agilent 2100 bioanalyzer (RNA Integrity Number [RIN] > 8). cDNA libraries were constructed using the TruSeq RNA Library Prep Kit (Illumina, San Diego, CA, USA) by Teragen Etex Bio Institute (Seoul, South Korea), and the libraries were sequenced on an Illumina HiSeq 2500 system. The gene expression levels were measured with Cufflinks v2.1.1 using the latest release of the Ensembl gene annotation database. To improve the accuracy of the measurements, the multiread correction and fragbias-correct options were applied; all other options were set to the default values. Transcriptome datasets used in the PCA were obtained from {"type":"entrez-geo","attrs":{"text":"GSE117664","term_id":"117664"}}GSE117664 (Yun et al., 2019, PSCs-derived differentiated cells from hESCs and hiPSCs) and {"type":"entrez-geo","attrs":{"text":"GSE73721","term_id":"73721"}}GSE73721 (Zhang Y et al., 2016, human brain-derived cells). Since hierarchical clustering exhibited clustered in accordance with study or platform, bias-corrected expression was carried out for data comparison. The DEGs were identified using Cuffdiff with a false discovery rate (FDR) < 0.05 and further screened by 2- or 4-fold changes of fragments per kilobase of transcript per million mapped reads (FPKM) in at least one sample of the group. The RNA-seq data are available from the NCBI GEO database (accession number {"type":"entrez-geo","attrs":{"text":"GSE130063","term_id":"130063"}}GSE130063).