We tested each antibody using formaldehyde crosslinked cells and had a two-step procedure for considering an antibody successful. (i) We tested all selected antibodies in batches, with each batch containing a mock-IGG (Santa Cruz) negative control and hnRNPH (Bethyl) positive control. Batches with variability in either the mock-IGG or hnRNPH controls were excluded and retested. For each successful batch, we computed enrichment for each lincRNA between the tested antibody and mock-IGG. We considered an antibody successful in the first step if the highest enrichment level exceeded a 5-fold change compared to the mock-IGG control and more than 10 lincRNAs exceeded this threshold. While this approach can yield false positives (antibodies that pass but are not efficient) it significantly reduced the number of antibodies to be tested in the next step. (ii) For all antibodies that successfully passed the first criteria, 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
