GSE168391
RNA sequencing profiles of control and PRPF19 knockdown TIG-3 cells
Total RNA was purified from TIG-3 cells transfected with siControl or siPRPF19 using miRNeasy Mini Kit (QIAGEN) with RNase-free DNase (QIAGEN). Library preparation, sequencing, and data analysis were performed by DNAFORM (Yokohama, Kanagawa, Japan). Quality and quantity of extracted RNA was assessed by NanoDrop 8000 Microvolume UV-Vis spectrophotometer (Thermo Fisher Scientific) and Agilent RNA 6000 Nano kit of BioAnalyzer 2100 System (Agilent Technologies). RNA-seq library was prepared using SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara Bio) following the manufacturer's instruction. In brief, ribosomal RNA was depleted employed RiboGone which included in the kit. After that, first strand cDNA synthesis was performed using N6 primer. The first-stranded cDNA was purified using equal volume of AMPure XP beads (Beckman Coulter). The purified cDNA was amplified into Illumina-specific RNA-seq libraries by PCR. The libraries were sequenced on a Hiseq sequencer (Illumina) to generate 150 nt paired-end reads. The quality of sequence data was first assessed using FastQC (ver. 0.11.7). Raw sequence reads were then trimmed and quality-filtered with Trim Galore! (ver. 0.4.4), Trimmomatic (ver. 0.36), and cutadapt (ver. 1.16) software. Trimmed reads were mapped to the human reference genome (GRCh38.p10) using STAR (ver. 2.6.1a). Overall design: RNA sequencing profiles of TIG-3 cells 3 days after transfection with siControl or siPRPF19.