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Old 10-07-2016, 06:38 AM   #1
anlun
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Location: Copenhagen

Join Date: Nov 2013
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Default RNA-Seq on clonal pools

Dear All,

I'm about to setup a transcriptome study based on RNA-Seq from a set of different CHO cell lines expressing different model proteins, to compare gene expression for a specific set of genes between the cell lines.
I’m working with CHO cell lines in suspension cultures. I have a few CHO cell line, which originate from a single clone. These I have experience with culturing and extracting RNA from to use in DE studies with great success.

However, a cell line that originated from a single clone is subjected to clonal variation since you in the selection process take one clone with specific properties (often high titer and growth).
Cell cultures consisting as a pool of several clones (the step prior to clone selection) gives a more reel picture of what can be expected regarding titer and growth profile for expression e.g. a specific model protein.

My plan was to run Illumina HiSeq2000 with paired end reads of 100bp and 30M.

My question goes; can I run a transcriptome study on cells coming from a clonal pool?
What do I need to consider? Is higher number of reads needed? What can be the drawbacks?


Sorry for my ignorance within the field of RNA-Seq and thanks in advance for your help.
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clonal pool, differential expression, rna-seq design

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