Using Agilent’s One-Color Quick Amp Labelling kit (5190-0442), we amplified and labelled total RNA for hybridization to prototype mouse lincRNA arrays (G4140-90040) according to manufacturer’s instructions with a few variations. The custom Agilent SurePrint G3 8×60K mouse array design used for this study (G4102A, AMADID 025725 G4852A) has probes to 21,503 Entrez genes and 2,230 lincRNA genes. A new updated version of this mouse design is commercially available that contains probes to 34,017 Entrez gene targets as well as 2,230 lincRNA genes (G4825A). The cRNA samples were prepared by diluting 200ng of RNA in 8.3ul water and adding positive control one-color RNA spike-in mix (Agilent, 5188-5282) that was diluted serially 1:20, then 1:25 and finally 1:10. We annealed the T7 promoter primer from the kit by incubating at 65°C for 10 minutes. We prepared the cDNA master mix and added it to the annealed RNA and incubated at 40°C for 2 hours, followed by 65°C for 15 minutes. We prepared the cRNA transcription master mix and added it to the cDNA and incubated at 40°C for 2 hours protected from
