GSM6008385: OPC WT; Mus musculus; RNA-Seq
GSM6008385
Total RNA was extracted from OPCs derived from mESCs using TRIzol Reagent (Invitrogen) and genomic DNA was removed using DNase I (Takara). Quality of samples were evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies) and qualified using the ND-2000(Nanodrop Technologies). An amount of 1μg total RNA was used for RNA-seq transcriptome library preparation following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA). After quantified by TBS380 (Picogreen), paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq 6000 platform sequencer (2 ×150bp read length). The raw paired end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software. The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/index.shtml?t=example). To identify DEGs (differential expression genes) via different groups, a list of differentially expressed genes was generated according to the transcripts per million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.