lincRNA probes on the Agilent microarray were analysed using the differential expression methodology described above after knockdown of the transcription factor and comparison to the negative control hairpins. To confirm the expression changes of these lincRNAs, we hybridized 12 transcription factor knockdowns on a custom lincRNA codeset using the Nanostring nCounter assay41 (LIN-MES1-96). The knockdowns were profiled in biological duplicate along with 15 negative controls. Regulated lincRNAs were identified using the differential expression approach described above.
