Antisense oligonucleotides gapmers with multiple targets

HeLa cells were transfected with seven different gapmer antisense oligonucleotides (Lipofectamine 2000; 50 nM; media change after 24h; 72h treatment time). Experiment was performed in triplicates with mock-transfected cells as negative control. RNA-Seq libraries were prepared using Illumina's TruSeq Stranded mRNA kit, and sequenced on Illumina HiSeq with paired end reads with length of 150bp each. Gapmers used in the study were LNA-DNA fully phosphorothioated gapmers, each (except 946 which is a neg.ctrl.) designed to target multiple HeLa expressed genes. Gapmer structures (E = 5meC): 000 - mock transfection 107 - base: TTCGCTCGTTGEE, sugar: LLDDDDDDDDLLL 108 - base: EGTTCAGGGTGGT, sugar: LLLDDDDDDDDLL 110 - base: EGCCATCTTCCEG, sugar: LLDDDDDDDDDLL 115 - base: GTGTCCACCTCCTG, sugar: LLLDDDDDDDDDLL 119 - base: AGGCTTTCCCACATTE, sugar: LLDDDDDDDDDDDLLL 124 - base: TGTAACACTCACCGCAAA, sugar: LLLDDDDDDDDDDDDDLL 946 - base: ECAAATCTTATAATAAETAE, sugar: LDLLLDDDDDDDDDDLLDLL