Global gene expression profiling from LeuCAG3'tsRNA depleted- HeLa and HCT-116 cell lines through 50 base pair paired-end RNA-seq

We sequenced mRNA expression from 3 HeLa and 3 HCT-116 cell lines transfected with LNA (Locked nucleic acid) GL2, LNA CAGMM, or LNA CAGPM respectively. In order to dissect the biological role of 3?tsRNAs (type I tsRNAs) in mammals, we reduced the bioavailable abundance of specific tsRNA species using complementary locked nucleic acid/DNA-mixed antisense oligonucleotides (LNA). The LNA forms a highly stable complex with the target RNA in a sequence specific manner, essentially inhibiting its ability to interact with their biological targets. In our tsRNA-knockdown experiments of HeLa and HCT-116 cell lines, we used three different LNA probes. GL2, is the LNA probe complementary to firefly luciferase gene from pGL2 vector (Promega, WI, USA), which serve as negative control. CAGPM, is the LNA probe perfect complementary to LeuCAG3?tsRNA. CAGMM, is the LNA probe complementary to LeuCAG3?tsRNA with 2 nt mismatches. The sequences for LNA probes are as follows. LNA bases are upper-case letter and DNA bases are lower ?case letter. GL2: GtaCgCgGaaTaCTtC CAGPM: tGTcAGgAgTggGaT CAGMM: tCTcACgAgTggGaT Examination of mRNA levels in individual HeLa and HCT-116 cell lines 24h after transfection of LNA GL2, LNA CAGMM, LNA CGPM respectively.