A good spike-in sample for ChIP-seq will depend on the protein of interest. If the protein of interest is found in another species like a histone modification, people will often add a controlled amount of sample from that species (usually Drosophila) and IP against the chromatin from both genomes simultaneously. Most importantly the genome of the spike-in sample must be divergent enough from your sample to be able to map most reads uniquely to the two reference genomes. You cannot work with a human sample and add a human spike-in sample. When the antibody of interest is only functional within the species of interest, it is necessary to add both a spike-in sample and a spike-in antibody that will be specific to the spike-in sample.
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