Can I use different cell lines of the same cell type from the same tissue?

[CharlesG]

Hi everyone,

I am an absolute novice to chip-seq and I have to plan a chip-seq experimnent involving the overexpression of a tanscription factor in microvascular endothelial cells from the skin and or lungs. So I have two conditions, control untreated and TF-overexpressed conditions. I plan to use 4 biological replicates per condition. It will be dificult to generate sufficient cell amounts from cells isolated from patients, so I want to purchase immortalised cell lines.

I wish to find out if using different cell lines of the same cell type from the same tissue is similar to having cells from different patients.

I will be very grateful for any clarification and also any link thank can help me plan my chip-seq experiement better.

Thank you in advance for your Kind help.

[Meyana]

If you are using different cell lines you are comparing just that, cell lines. Not patient-derived samples. You cannot infer that their "diversity" will mimic that of patients-derived cells, nor can you be sure they even respond similarly to patient-derived cells.

So, you are suggesting a project on how different cell lines respond to overexpression of your TF of interest.

If you want to pursue patient cells, it may be better to try and optimise conditions for them in the lab to grow them maybe a few doublings (I have never worked with endothelial cells, I don't know how easy it is) or you should obtain precurser cells which you might be more able to get to expand in the lab and differentiate them in vitro and work with those.

FYI, there are methods out there for doing ChIP-seq from very low cell numbers which appears to give quite nice results, may want to explore that.