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We are setting up a series of ChIP-seq and RNA-seq experiments from a few different cell lines with control and experimental samples for each. The following refers to biological replicates:
1. RNA-seq will all be done in triplicate. For ChIP-seq, will triplicate provide much of a benefit over duplicate? (eg. see ENCODE guidelines vs http://www.ncbi.nlm.nih.gov/pubmed/24688750)
2. Should ChIP-seq input samples be replicated? If the IP samples are done in triplicate would singles or duplicates be ok for input?
3. Everything will be sequenced at the same facility, is it important that everything is done at the same time? For example, is it better to wait until all replicates for all samples are ready and sequence them all in the same run, or could we sequence replicates as they are ready? The ChIP and RNA will at least likely be run separately because of single- vs paired-end reads.
1. RNA-seq will all be done in triplicate. For ChIP-seq, will triplicate provide much of a benefit over duplicate? (eg. see ENCODE guidelines vs http://www.ncbi.nlm.nih.gov/pubmed/24688750)
2. Should ChIP-seq input samples be replicated? If the IP samples are done in triplicate would singles or duplicates be ok for input?
3. Everything will be sequenced at the same facility, is it important that everything is done at the same time? For example, is it better to wait until all replicates for all samples are ready and sequence them all in the same run, or could we sequence replicates as they are ready? The ChIP and RNA will at least likely be run separately because of single- vs paired-end reads.