What are the suggested positive controls?
One is the IVT control. Here, the IVT starting material is 250 ng of the pTRI-Xef linearized plasmid provided with the Ambion IVT kit. If not using the kit, an appropriate amount of a dsDNA template that contains the pT7 promoter, with prior history of use as a successful T7 RNA polymerase template, should be used. Yields should typically range from 100-140 ug, limited by exhaustion of the nucleotides in the reaction mixture and the rated 100 ug binding capacity of the Qiagen RNeasy column. Visualization on a non-denaturing agarose gel should yield two intense bands ~0.9 kb and ~1.5 kb.. The other is the whole TLAD protocol control. This control will enable the user to distinguish sample-specific problems from protocol implementation issues. Here, the starting material is 50 ng of blunt-ended PCR product in the 100-1000 bp range (preferably around 200-500 bp). If this protocol is used as part of a ChIP-chip experiment, and if troubleshooting RNase A handing and CIP treatment, the PCR p
