For context: 1.8e5 C2C12 cells in 6 well. Around 1 - 2 ug of plasmids transfected the next day using Jetprime. Cells were grown for 1 more day.
I used to use trizol then DNAse with 20 U for 15-20 mins at RT, and it worked somewhat. There were still some contamination but the Cq is 10+ units different between -rt and +RT so I accepted it.
I realized that I needed to clean up my samples after DNAse using a kit anyway and I disliked phenol / chloroform in general because of the waste so I decided to bite the bullet and got a kit (NEB miniprep). It really cut my prep time significantly and I can process 30 samples within 5 hours instead of 15 for a whole day.
The big problem is I found there is lots of plasmid left in my rna. Sometimes Cq of -rt is the same as +RT. I followed NEB protocol. This kit has a gDNA removal column AND on column DNAse but seems like it didn't work so well. Now I have to DNAse again and clean up. Maybe my DNAse doesn't work, I haven't tested it though.
Tldr: DNAse treatment sucked and I need to know from experienced people how long and how much DNAse to use for the on column treatment.