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In this episode of the Epigenetics Podcast, we talked to Claudio Cant\xf9 from Link\xf6ping University about his work on peak blacklists, peak concordance and what is a peak in CUT&RUN.\nOur host Stefan Dillinger and guest Claudio Cant\xf9 dive into the topic of when we can be sure that a peak is a peak. To help with this, Claudio Cant\xf9's group has been working on defining a set of suspicious peaks that can be used as a "peak blacklist" and can be subtracted to clean up CUT&RUN data sets. The lab also worked on a method called ICEBERG (Increased Capture of Enrichment By Exhaustive Replicate aGgregation) to help define peaks from a number of experimental replicates. By using this algorithm, the team is trying to discover the beta-catenin binding profile, not the tip of the beta-catenin binding iceberg, but the whole of the beta-catenin binding profile.\n\xa0\nReferences\n\nZambanini, G., Nordin, A., Jonasson, M., Pagella, P., & Cant\xf9, C. (2022). A new CUT&RUN low volume-urea (LoV-U) protocol optimized for transcriptional co-factors uncovers Wnt/\u03b2-catenin tissue-specific genomic targets. Development (Cambridge, England), 149(23), dev201124. https://doi.org/10.1242/dev.201124\n\n\nNordin, A., Zambanini, G., Pagella, P., & Cant\xf9, C. (2022). The CUT&RUN Blacklist of Problematic Regions of the Genome [Preprint]. Genomics. https://doi.org/10.1101/2022.11.11.516118\n\n\nNordin, A., Pagella, P., Zambanini, G., & Cantu, C. (2023). Exhaustive identification of genome-wide binding events of transcriptional regulators with ICEBERG [Preprint]. Genomics. https://doi.org/10.1101/2023.06.29.547050\n\n\xa0\nRelated Episodes\n\nChromatin Profiling: From ChIP to CUT&RUN, CUT&Tag and CUTAC (Steven Henikoff)\n\n\nSingle Cell Epigenomics in Neuronal Development (Tim Petros)\n\n\xa0\nContact\n\n\nEpigenetics Podcast on Twitter\n\n\nEpigenetics Podcast on Instagram\n\n\nEpigenetics Podcast on Mastodon\n\n\nActive Motif on Twitter\n\n\nActive Motif on LinkedIn\n\n\nEmail: podcast@activemotif.com