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I have some samples ready to sequence but I having some doubts about the number of inputs to sequence.
The samples come from 2 human cell lines, the same original line but each stably expressing a modified factor (from a BAC), and for each cell line there are 2 biological replicates of:
Input
GFP ip
Pol II ip
The inputs will be sequenced at ~60M the IPs ~30M and there is one input per cell line per replicate. I will sequence one input of each cell line but I don't know whether to sequence both input replicates per cell line - it seems like an overkill.
What do you suggest?
Also, are 30M reads (75 bp, SE) for the ips too much? I have no expectations about the profile of the ChIPed factors.
Thanks
The samples come from 2 human cell lines, the same original line but each stably expressing a modified factor (from a BAC), and for each cell line there are 2 biological replicates of:
Input
GFP ip
Pol II ip
The inputs will be sequenced at ~60M the IPs ~30M and there is one input per cell line per replicate. I will sequence one input of each cell line but I don't know whether to sequence both input replicates per cell line - it seems like an overkill.
What do you suggest?
Also, are 30M reads (75 bp, SE) for the ips too much? I have no expectations about the profile of the ChIPed factors.
Thanks