Bulk RNA-seq of cell line: Sample 4LN-B_rna
RNA from melanoma cell lines grown in vitro were extracted using Qiagen Rneasy Plus columns.The RNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific) and RNA integrity was checked using TapeStation (Agilent Technologies). The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer's instructions (New England Biolabs). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94°C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3'ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). Final libraries were sequenced on a NovaSeq 6000 with S4 flow cell with 2x150 bp paired-end sequencing.