For HEEBO microarray experiments, poly - adenylated RNAs were amplified in the presence of aminoallyl - UTP with Amino Allyl MessageAmp II aRNA kit (Ambion).
Inclusion of modified amino - allyl dUTP at a ratio of 3:2 with unmodified dUTP in the in - vitro transcription reaction generated antisense RNA (aRNA) capable of chemically coupling to amine reactive dyes.