We are doing research on the effects of non-coding RNAs in DNA repair.
We are checking for splicing defects after knockdown of different non-coding RNAs. In addition we want to evaluate potential off-target effects, and cellular effects of the used siRNAs and GapmeRs.
Samples are from a immortalized human female cell line (U2OS). Cells were transfected with siRNA/GapmeR. Cells were harvested, RNA was extracted by trizol protocol. total RNA was depleted of rRNA using Lexogen Corall RiboCop kit. Sequencing library was prepared using Lexogen Corall Total RNA-seq Library Preparation kit. Samples were spiked before rRNA depletion with ERCC spike in from Thermo. 3 biological replicates per treatment condition.