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I am going to be tracking changes in methylation status of cells over time and with varying treatments. For MBD seq do I need to sequence a corresponding input reaction for every time point and treatment or can I compare the different groups to each other instead? I will be analyzing untreated time point one as a baseline. Would this suffice?
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In general when we're doing this type of enrichment work we only do a single input sample using the same conditions as for the enriched samples. Most of the artefacts come from the DNA preparation, mapping and sequencing stages and won't change between timepoints or treatments (unless you have a treatment which is going to grossly change the structure of your DNA in some way). Doing a matched input for each sample would get really expensive really quickly!
In some cases we don't bother doing an input at all but just use data from previous inputs we've run to either use in the analysis or to provide sets of regions which we should ignore.
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