Differential lncRNA expression upon hypoxia affects splicing efficiency

RNA sequencing was performed to identify long non-coding RNAs that are dysregulated upon hypoxia in breast cancer. Subsequently, the effect on splicing effiency (intron retention, exon skipping …) was investigated from RNA sequencing analysis upon knockdown of the candidate lncRNA and upon hypoxia. Overall design: Cells were treated with GapmeRs or tetracycline-inducible shRNAs against the candidate lncRNA and cultured upon hypoxic conditions (1%O2). Additionally, cells were treated with shRNAs against SART3 or GFP.