To control for ‘off-target’ effects, we analysed additional hairpins against the 26 lincRNAs affecting Nanog-Luciferase levels. Of the 26 lincRNAs, we identified 15 lincRNAs that contained an additional hairpin that reduced lincRNA expression by >50%. V6.5 ESCs were infected with the best and additional hairpin across biological replicates for these 15 lincRNAs and 21 negative control hairpins. RNA was extracted after 8 days and Oct4 expression levels were determined using qPCR. Significance was assessed relative to the negative controls using a one-tailed t-test.
