Illumina small RNA ladder and NEB miRNA marker

[lostviking]

Hi all,

I have a question about the accuracy of the Illumina SRA ladder (20nt-100nt) that is used when making small RNA libraries.

I have been running the microRNA marker from NEB (#N2102S) next to the Illumina SRA ladder and I am getting some weird results: the 17nt band is migrating slower than (or at least equal to) the 20nt band of the SRA marker, the 21nt band is sitting well into the twenties and the 25nt band of the NEB marker is just shy of 30nt compared to the SRA ladder. The migration pattern is quite reproducible, even after ethanol precipitating the NEB marker and loading it in on the gel using Illumina's own loading buffer.

I think one of these two markers must be migrating at the wrong rate.

Has anyone had a similar experiences with either of these markers?

Cheers

[Manna]

The internets don't seem to have any pictures of what this ladder looks like (Illumina SRA ladder). I have this ladder in my freezer, and I just ran a gel with it, not terribly concerned about needing to find a picture later. This unanswered seqanswers question is the only thing I can find where it is even mentioned. Was it discontinued because it is crap? I looks ok on the gel, but running it next to a smear, I'm not sure if I should scrap this & start again tomorrow with a more legit ladder or what.

Sorry - all I really need to know is what this ladder looks like on a gel. Anyone got an annotated pic?

Thanks,
M

[mama]

The Illumina SRA ladder is a DNA ladder and the microRNA marker from NEB is a RNA ladder. That's the reason why they don't migrate the same way.