SK-BR-3 RNA sequence
Total RNA was converted to cDNA using oligodT primers.  To prepare sequencing libraries by ligation cloning, 100ng-1ug of DNA was acoustically sonicated to 300bp or 500bp using the Covaris Sonicator S220. Libraries were constructed using NEBNext DNA library Prep Master Mix Set for Illumina (New England Laboratory, #F6040L) for end-repair, 3’adenylation and ligation according to manufacturer’s instructions.  MinElute PCR Purification Kit (Qiagen, #28006) is used for the purification step during library prep.  Agarose electrophoresis is run for excision at 300 or 400 bp for size selection. We then performed 8 cycles of PCR following manufacturer’s direction, using PE5/7 primers (Illumina Inc). Agencourt AMPure XP (Beckman Coulter, #A63881) were used for final purification. Final concentration was measured by quantitative PCR using KAPA Library Quantification Kit (KAPA Biosystems, KK4835) and ABI PRISM real-time machine (Applied Biosystem 7900HT), as well as 2100 Bioanalyzer (Agilent).