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Old 05-06-2011, 10:17 PM   #1
Location: China Xian

Join Date: Jan 2011
Posts: 11
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, 08:34 AM   #2
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Location: Boston

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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:

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

Linear amplification of RNA:
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Old 05-09-2011, 04:47 PM   #3
Location: California

Join Date: May 2008
Posts: 40

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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porcine, transcriptome

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