It mostly depends on the downstream analysis.

Different methods of extracting small RNAs from cells or tissues are available, most of them are modifications of the acid guanidinium thiocyanate-phenol-chloroform extraction method developed by Chomczynski and Sacchi (Chomczynski and Sacchi 1987) which is now commonly known as Trizol (Life Technologies) or Qiazol (Qiagen) extraction methods. They are more or less equivalent for brain. We routinely use Qiagen kits, to extract small RNA, but we don't purify smallRNAs from total RNA, since we mostly used this method for RT-PCR.

If you need the size purification of small RNAs from total RNA. This step has been initially done by gel electrophoresis (Elbashir et al. 2001), or by immunoprecipitation of small RNA-bound proteins (Mourelatos et al. 2002; Dostie et al. 2003). The commercially available kits to isolate small RNA from total RNAs typically combine the Chomczynski and Sacchi method with a size-purification step through the binding and subsequent elution of RNA of specific size ranges from a column. The choice of the best method is mostly dependent on the type of downstream analysis.

Dear Davide Tonelli,

Thank you for your reply. I want to detect miRNAs by real time PCR...

I've had very good luck with the Ambion Mirvana kit, following the protocol for total RNA extraction.

I want to isolate miRNA for deep sequencing. Plz suggest the best kit.

Thanks