I would like to ask you if you can tell me about the 3 different background primer: in which chromosome and in which position have they been done?

Hi Maria, sorry, I don't think I have that information handy. The other two authors, Yasu Shima and Erin Clark have left the lab and I am not sure where to look for that information. However I am virtually positive that they are intergenic regions and were selected as regions that have essentially no signal in any sample. Almost any such regions will do. In addition, the sequences are given so you should be able to find the regions we used, if that is important to you. For example, I blasted the first primer pair and found that it brought up a region intergenic near mdh1 at 11:21526242-11:21526185. Looking at bigwigs of several of our samples in this region, I see no appreciable signal. This is the kind of region you want, so that you can estimate enrichment for highly open peaks (e.g. near the TSS of housekeeping genes).

Hope this helps. best, Sacha

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