we performed immunoprecipitation on two additional biological replicates along with 4 mock-IGG controls. We computed a t-statistic for each lincRNA compared to the controls and assessed the significance using a permutation test, by permuting the samples and IGG samples (as above). Hits were considered significant if they exceed a t-statistic cutoff of 2 (log scale) compared to the controls and had an FDR<0.2. We allowed a slightly higher FDR cutoff since the number of permutations was far smaller yielding lower power to estimate the FDR. Only antibodies yielding significant lincRNAs were considered successful. In total, we identified 12 of the 28 complexes (55 antibodies) with at least one successful antibody.
