For the ChIP-seq in the ROSMAP study (syn4896408), there are several (12) controls listed in the bam files, some of which include: NC-Pool-1, NC-Pool-1_8plex, PC-Pool-1, PC-Pool-1_8plex. In the manifest, these are all labeled as H3K9ac, but since all the files were listed this way I was wondering: 1) Are these actually ChIP samples? Are any of them actually IgG or genomic controls, as in are these samples that should have little to no enrichment to be used for peak calling? 2) Either way, what actually does the PC/NC mean? Thanks so much!

Created by bhwang503
PC means positive controls. These samples are anti-H3K9ac ChIPs pooled from different subjects. NC means negative controls. These samples are pooled genomic DNA. There should not be any peaks. Please feel free to contact Hans Klein at Broad (hklein@broadinstitute.org) if you have further question. Best Lei
Hi @bhwang503, thank you for you question! @leiyu do you know the answer to this question? Ben

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