Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, Singapore
In our experiments, we used RNeasy plus mini kit (QIAGEN) to extract the total RNA. We also tried to this protocol on total RNA, it worked. However, please note that m6A is also found in rRNA, tRNA and snRNA.
I have limited experience with this protocol. It seems that the mRNA quantity is very important. 20 ug mRNA perhaps is the lower limit for decent signals. I imagine that you would need 200 ug total RNA to have the same amount of signal. Why don't you try Trizol and let us know the results.