Using our previous catalogue of K4-K36 defined lincRNAs2 along with the reconstructed full-length sequences we determined using RNA-Seq3, we designed shRNA hairpins targeting each lincRNA identified in both sets. Specifically, we used the conservative K4-K36 definitions from our previous work2 that were expressed in mouse ES cells. We further filtered the list to include only multi-exonic lincRNAs that were reconstructed in mouse ES cells3. Together, this yielded 226 lincRNA genes.
