I'm having some trouble obtaining an RNA 200-500 base fragment size in lysates from cells fixed with 1% formaldehyde. I've based the parameteres of my protocol on the Covaris protocol for Total RNA in 130 ul snap tubes (attached), however, this protocol is for pure, unfixed RNA. With all the parameters the same, I've increased treatment time up to 30 minutes, but I am still getting average fragment sizes far beyond 1000 bases. Which parameters would be best to vary to obtain the desired size?

Thanks