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Old 05-06-2011, 09:17 PM   #1
ips
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Question Help for experimental design

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?
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Old 05-09-2011, 07:34 AM   #2
pbluescript
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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....na-seq-system/

Modified Illumina RNA-Seq protocol (look in the supplemental data):
http://www.plosbiology.org/article/i...l.pbio.1000590

Linear amplification of RNA:
http://www.jove.com/details.stp?id=2634
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Old 05-09-2011, 03:47 PM   #3
monad
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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!
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