Hello! new on NGS

[Verenais]

Hi all!

I am planning to request a RNA-Seq service from a local provider, but I am not clear about the following things:

If I just want to compare the global gene expression of two CHO cell samples, are 50 bp single sequence reads good enough for the analysis? or paired end reads are required?

In the GAIIx system, is one lane enough to run two different CHO mRNA-libraries, considering that the CHO genome contains around 24,000 genes?

Which system is better GAIIx or HiSeq2000?

Thank you, hope someone with experience on this can give me some advice!

Verenice.

[gringer]

The answers to these questions probably depend on how much money you are prepared to spend -- "good enough" is different for different people. If you want the best results, use paired-end sequencing with as many reads as possible.

[Verenais]

Thank you gringer!

You are right, first of all I need to consider my budget for this analysis.

Have a nice day!