Comprehensive Multi-omics Profiling of Cell Lines

Small RNA-seq libraries were prepared by using 50 ng of total RNA, isolated from parental cell lines, as input and the NEXTflex Small RNA Library Prep Kit v3 (Bio Scientific) or by Novogene (Hong Kong). Sequencing was performed on an Illumina HighSeq platform at the Deep Sequencing Group (TU Dresden) or Novogene. For mRNA-seq libraries, polyA-RNA was enriched using oligo(dT) beads. Generation of libraries and sequencing were performed by Novogene on an Illumina HiSeq platform. RNA-seq and miRNA-seq data were analyzed as described previously (22 (link),23 (link)). RNA-seq data of the TCGA cohorts were obtained from the GDC portal (https://portal.gdc.cancer.gov).