To determine if lincRNA hairpins were effective at knocking down the lincRNA of interest, we infected each hairpin into mouse embryonic stem cells, selected for lentiviral integration, and measured changes in the targeted lincRNA expression level. We isolated total cellular RNA after 4 days; this time-point was chosen to allow for identification of robust changes while minimizing secondary effects due to differentiation of the ES cells. We reasoned that this would allow us to determine more direct effects due to RNAi rather than to differentiation.
