When performing ChIP-qPCR I always bring along an Input sample for each treatment condition and fixing method. For sequencing, I'm wondering whether I could drop the Input samples for cells fixed with FA-only and sequence the input samples from cells fixed with FA/DSG. I would then use this Input as a control for all samples (same cell lines used through-out).
I don't understand your setup. How many samples , control et6c. What is the DSG?
Input sample provides correction for many biases such as efficiency of sonication or nuclease digestion across the genome . I would keep at least one input for each method of fixation used. A low depth sequencing could suggest if your target regions are susceptible to fixation bias.
Input samples should be material treated exactly the same way as your ChIP samples but without IP. So you subject them to the same crosslinking, extraction, sonication conditions and reverse-crosslinking. It is best to include an input sample for every treatment, reason being that your treatments might induce a lot of changes in the chromatin that result in a lot of false positives if you don't have the appropriate controls.
Thank you all for answering my question, its very much appreciated. I was thinking along the same lines but wasn't 100% sure. Thanks again.
Fragmentation bias the biggest problem associated with differential crosslinking conditions, but the Walleed's point is good. If your IP's were performed from two different inputs then you will absolutely need to sequence both.
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