RNA sequencing of non-targetting ASOs on HEK293 and U2OS cells

Non-targetting ASOs are commonly used as negative controls in vitro and in vivo. Here, we compare the transcriptomic profile of HEK293 and U2OS, following 3 days treatment with 3 different non-targetting ASOs. In those conditions, we did not find major transcriptomic changes following ASO treatment, confirming that they are appropriate negative controls. Overall design: The experiment was performed using 2 different cell types (HEK293 and U2OS) and 3 non-targetting ASOS (CTRL1, CTRL2 and CTRL3). Splice switching ASO (SSO) does not have an endogeneous target in U2OS and is used as a fourth non-targetting ASO in this cell line. Untreated samples (both HEK293 and U2OS) are included in the analysis as well. Each sample was prepared four times in total (2 replicates on 2 independent experiments). All ASO treatment were performed for 3 days at 1uM. 36 samples total. U2OS and HEK293 treated with control (non targetting ASOs called CTRL1, CTRL2, CTRL3 and SSO) ASOs or untreated. 4x HEKs -CTRL1, 4x HEKs -CTRL2, 4x HEKs- CTRL3, 4x HEKs untreated, 4x U2Os -CTRL1, 4x U2Os -CTRL2, 4x U2Os- CTRL3, 4x U2Os untreated, 4x U2OS- SSO.