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  • 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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