hairpins targeting 147 lincRNAs, including 10 with a second best hairpin, and 40 protein-coding genes in biological replicate. The hairpins and their replicates were randomly distributed across 7 96-well plates and prepared in batches. Each RNA preparation batch contained 1 pLKO hairpin and 1 clonetechGfp_437s1c1 hairpin in a random location on the plate. To minimize batch effects, the plate locations of the biological replicates were scrambled and the positions within the plates were scrambled for all hairpins and replicates.
