RNA was extracted from flash frozen biopsies using AllPrep DNA/RNA/protein Extraction Kit (Qiagen) according to manufacturer's instructions. In brief, tissue biopsies was cut into smaller pieces and submerged in lysis buffer. Extraction was done on a QIAcube liquid handling system (Qiagen). After extraction, RNA was quantified and analyzed for purity and size distribution using a Bioanalyzer (Agilent). For RNA sequencing, 200 ng input RNA was used for preparing RNA sequencing libraries, which was done using TruSeq Stranded Total RNA Library Prep Kit (Illumina) following manufacturer's instructions. Briefly, RNA was denatured and ribosomal RNA (rRNA) was removed using Ribominus Gold (Illumina). After cleanup, RNA was fragmented and 1st and 2nd strand synthesis performed. Finally, libraries was adaptor ligated and amplified. AMPure XP beads was used for cleaning up the prepared sequencing libraries and quantification was done using a Qubit fluorometer (Thermo Fisher). Sequencing libraries was paired-end sequenced (2x125 bp) on the Illumina HiSeq2500 platform. Sequenced reads was trimmed and mapped to hg19/GRCh37 reference genome using BWA-MEM v0.7.12 software. Stranded Total RNA Library
GEO Accession
GSM3963752