What's your recommended RNA fragmentation method?

[nasobema]

We already tried
- just heat (95°C)
- Mg2+ based buffer with heat
- Zn2+ based buffer with heat

The results were very different with the experiences for Zn2+ (ZnCl2) containing buffer.

Is it also possible to nebulize RNA? How would the fragments look like, I mean does this method affect ligation to RNA adapters?

[chinahnzj]

hi, Why not try to use ultrasonic?

[nextgen]

RNA fragmentation

Hi:

What is your result with either Mg2+ or Zn2+ based buffer? I prefer Mg2+ based buffer but can't find any protocol. thanks,

We already tried
- just heat (95°C)
- Mg2+ based buffer with heat
- Zn2+ based buffer with heat

The results were very different with the experiences for Zn2+ (ZnCl2) containing buffer.

Is it also possible to nebulize RNA? How would the fragments look like, I mean does this method affect ligation to RNA adapters?

[sjm]

I like the potassium and magnesium acetate salts + heat method in Mortazavi et al., Nat Methods 2008. Zymo RNA Clean and Concentrator columns make a nice alternative to purifying your RNA afterward on Sephadex.