Currently I am working on a project to find the most optimal protocol for doing ChIP-seq on frozen tissues. Most protocols are designed for cell lines, however, ChIP-seq in vivo (small biopsies for example) is really interesting to me. Especially differences in transcription factors and histone modifications between various tissues are of great value for functional annotation of genes.
I have found a promising protocol with very low-input that targets RNA Pol II. My question to you is whether the input is always lower when you target RNA polymerase. I have no experience doing ChIP targeting anything else than TF and histone modifications.
Also, if anyone of you works with a certain protocol that works well, is easy, cheap, or has low input, could you please share this with me?
Thank you so much in advance!
Kind regards, Eva