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Can I simulate different patients by using different cell lines of the same cell type and from the same tissue? Can I also study apoptosis in an immortalised cell line?

I have a gene X (transcription factor) which from wet lab experiments induces apoptosis in cell type A (endothelial cells) and proliferation in cell type B (smooth muscle cells).

I want to address this differential behaviour using ChIP-seq of antibodies against gene X.

I do not have enough patient samples and I wish to purchase immortalised cell lines to perform ChIP-seq with 4 biological replicates per condition: untreated control and over expression of X.

I plan each biological replicate to be a different cell line of the same cell type and preferably the same tissue. Is it possible to have such?

I will also be very grateful if anyone provides me a link or good article containing the best practices in planning for a ChIP-seq experiment.

Thanks in advance.

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  • $\begingroup$ It is difficult to say anything conclusively unless we know what kind of cells you are talking about. $\endgroup$ – WYSIWYG Jul 10 '19 at 8:40
  • $\begingroup$ @ WYSIWYG Thank you for your response. I will use microvascular endothelial cells from the skin and or lungs. $\endgroup$ – Charles Jul 10 '19 at 8:41
  • $\begingroup$ Can you please edit your question to add this information? And do you plan to use cell lines like lung/skin cancer as a proxy? $\endgroup$ – WYSIWYG Jul 10 '19 at 8:42
  • $\begingroup$ @WYSIWYG Please I am completely new to Chip-seq and I do not properly understand the meaning of "proxy" in this context. But I think I will only be using non-cancerous cell lines from the skin or the lungs. $\endgroup$ – Charles Jul 10 '19 at 8:54
  • $\begingroup$ I used "proxy" in a general sense. Using something in place of the other (a substitute that is expected to represent the original condition). In your case, the cell lines being proxy for the patient samples. There are commercially available human microvascular endothelial cells. Are you planning to use them? $\endgroup$ – WYSIWYG Jul 10 '19 at 8:59

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