Help for experimental design

[ips]

We proposed to detect the transcriptome/mirnaome of inner cell mass of porcine.The bottleneck for this study is that we could get very few cells ( about 10 from each blastocyst,~10 blastocyst for each fertilized porcine.We prepared 5 pigs for this experiment. So, we could get ~ 500 cells. ) Is so many cells enough for transcriptome/mirnaome analysis by Illumina Hiseq 2000? What else is worthy of note?

[pbluescript]

Here are a couple links to resources for amplifying small amounts of RNA. I have used the first two, and they work well.

Nugen Ovation RNA-Seq:

http://www.nugeninc.com/nugen/index.cfm/products/amplification-systems/ovation-rna-seq-system/

Modified Illumina RNA-Seq protocol (look in the supplemental data):

http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000590

Linear amplification of RNA:

http://www.jove.com/details.stp?id=2634

[monad]

DSN protocol really works. We used non detectable amount of total RNA as an input for library prep and got ~30M passing reads from single GAIIx lane. Unique read was ~5M, so higher redundancy as you expected from extremely low input material, but this was great!