Hi everyone. I am a new one in ChIP-seq and planning to do it for a poorly characterized TF. We are going to do ChIP on transfected HEK293 cells with WT and 2 other mutant forms of our specific gene which makes three samples to be sequenced. Regarding the negative control "Input DNA", the amount of samples for NGS would be 6 samples (1 sample+ its corresponding input DNA) which is quite expensive for us. As I am searching to find a way to reduce the cost, I was wondering that if its possible to find the sequencing RAW files of control DNA for HEK cell somewhere in databases and use it as a control to normalize the analysis. Is it possible? Are there such kind of data available and if so, can we use them instead of input DNA? As I understood the sonication is not a truly random process and we may have to sequence each samples's input DNA separately.Am I correct? If so, can we sequence only one of the input DNAs (for example WT) as the control for all the three samples or we have to consider one seperate input DNA for each sample?
I am looking forward to hearing from you.