Transcriptome Profiling of BRAF Mutant Cells

RNA was extracted from the THLE-2 cells after 48 h from cell transfection with N-Terminal p3XFLAG-CMV plasmid (Sigma-Aldrich, Saint Louis, MO, USA) and with plasmid containing BRAF WT and BRAF V600E using RNA extraction kit NucleoSpin RNA (Macherey-Nagel, Düren, Germany). Changes in gene expression were quantified using DNB-SEQ 30M PE100 reads sequencing by BGI Genomics (Shenzhen, China). Fastq files were aligned to reference genome GRCh38 using STAR aligner [77 (link)]. Read counts were created using GENCODE v34 and featureCounts [78 (link)]. Differentially expressed transcripts were determined using DESeq2 [79 (link)] using a false discovery rate (FDR) of 0.1.