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.
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.