
Dear All,
 
I am 
trying to use next-generation sequencing platforms to 
profile gene expression patterns during embryogenesis in our fish model 
(about 36 different stages). The genome of our model is about 2000 Mb. 
Currently only a draft of the genome with 70% coverage is available. I 
am considering using the following strategies to carry out our project:
1.       Use
 SMRT of Pacific Biosciences, TMS of Helicos, SOLiD3 of ABI, Genome 
Analyzer of illumina or other RNA-Seq methods to directly sequence RNA 
isolated from embryos at each stage. 
2.       Combine
 RNAs from embryos at different developmental stages to form an RNA 
pool. Use DSN treatment to get the normalized cDNA, use illumina to 
sequence this normalized cDNA and get a high coverage cDNA database. 
Then use SOLiD 3 SAGE to profile gene expression patterns, which the 
tags will be mapped onto the cDNA database firstly.
 
I need advice about which strategy is better? And how shall I set up biological and technique replicates? 
 
Thanks a lot for any thoughts or advice.

Sincerely Yours

Ziping
 		 	   		  
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