What is the source of your starting material?

For our laser captured neuronal cells we use the RNAqueous Micro Total RNA Isolation Kit from Ambion and for RT rxns the TaqMan microRNA RT kit from Applied Biosystems which requires a minimum of 1ng of input total RNA. Agilent also makes a small RNA chip to run on the Bioanalyzer if you are looking for greater resolution.

I have also looked at characterizing circulating miRNA in serum (fairly low yield) using Exiqon's miRCURY RNA Isolation Kit for Biofluids which has given me pretty reliable results. 

Here's a paper that describes a miRNA and next-gen sequencing protocol: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4138881/ 

Good luck!

Our lab uses the Qiagen RNease micro kit, which is especially designed for small input. I don't know what your sample looks like, but it works quite well for isolation from ~50,000 cultured cells. 

Each of my samples contains only about 5000 cultured cells. And I used the Qiagen kit you mentioned too, but we could not obtain enough amount of total RNA to generate a good library for sequencing.

After using the Qiagen RNA isolation kit you can use their PreAmp kit to amplify your RNA before cDNA synthesis.

Do you mean this kit:

miScript PreAMP PCR Kit

http://www.qiagen.com/de/products/catalog/assay-technologies/mirna/miscript-preamp-pcr-kit/

If yes, it is for qRT-PCR not miRNA sequencing. It states that "The miScript PreAMP PCR Kit uses highly multiplex, PCR-based preamplification of up to 400 miRNA-specific cDNA targets in one reaction."

Do you know any other pre-amplification kit for small RNA seq (other than those above, in my question)? Have you had any experience with it?

I recently found out about a kit from Clontech called the Nucleospin miRNA kit (Catalog number 740971 at www.Clontech.com), and they sent us a free sample for 10 miRNA isolations. It specializes in isolating miRNA, so this might be a way to improve your yield, and if they are willing to offer you a free sample to try it out, you might give that a shot. 

Thanks Breanna

Anyone knows how to amplify a very limited amount of miRNA for NGS sequencing, not qPCR analysis?

hi everyony nice to read above discussion. is it  possible amplify miRNA without kit , any method based on poly A polymerase? not getting results in this , using it for qPCR after RT reaction using usual reverse transcriptase ?