Claudio Cantù's guest appearances

Claudio Cantù

Epigenetics Podcast

OwlTail

In this episode of the Epigenetics Podcast, we talked to Claudio Cantù from Linköping University about his work on peak blacklists, peak concordance and what is a peak in CUT&amp;RUN. Our host Stefan Dillinger and guest Claudio Cantù dive into the topic of when we can be sure that a peak is a peak. To help with this, Claudio Cantù'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&amp;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.   References  Zambanini, G., Nordin, A., Jonasson, M., Pagella, P., &amp; Cantù, C. (2022). A new CUT&amp;RUN low volume-urea (LoV-U) protocol optimized for transcriptional co-factors uncovers Wnt/β-catenin tissue-specific genomic targets. Development (Cambridge, England), 149(23), dev201124. https://doi.org/10.1242/dev.201124   Nordin, A., Zambanini, G., Pagella, P., &amp; Cantù, C. (2022). The CUT&amp;RUN Blacklist of Problematic Regions of the Genome [Preprint]. Genomics. https://doi.org/10.1101/2022.11.11.516118   Nordin, A., Pagella, P., Zambanini, G., &amp; 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     Related Episodes  Chromatin Profiling: From ChIP to CUT&amp;RUN, CUT&amp;Tag and CUTAC (Steven Henikoff)   Single Cell Epigenomics in Neuronal Development (Tim Petros)     Contact   Epigenetics Podcast on Twitter   Epigenetics Podcast on Instagram   Epigenetics Podcast on Mastodon   Active Motif on Twitter   Active Motif on LinkedIn   Email: podcast@activemotif.com   

In this episode of the Epigenetics Podcast, we talked to Claudio Cantù from Linköping University about his work on peak blacklists, peak concordance and what is a peak in CUT&amp;RUN. Our host Stefan Dillinger and guest Claudio Cantù dive into the topic of when we can be sure that a peak is a peak. To help with this, Claudio Cantù'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&amp;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. References <ul><li> Zambanini, G., Nordin, A., Jonasson, M., Pagella, P., &amp; Cantù, C. (2022). A new CUT&amp;RUN low volume-urea (LoV-U) protocol optimized for transcriptional co-factors uncovers Wnt/β-catenin tissue-specific genomic targets. Development (Cambridge, England), 149(23), dev201124. <a href="https://doi.org/10.1242/dev.201124" rel="nofollow" target="_blank">https://doi.org/10.1242/dev.201124</a> </li> <li> Nordin, A., Zambanini, G., Pagella, P., &amp; Cantù, C. (2022). The CUT&amp;RUN Blacklist of Problematic Regions of the Genome [Preprint]. Genomics. <a href="https://doi.org/10.1101/2022.11.11.516118" rel="nofollow" target="_blank">https://doi.org/10.1101/2022.11.11.516118</a> </li> <li> Nordin, A., Pagella, P., Zambanini, G., &amp; Cantu, C. (2023). Exhaustive identification of genome-wide binding events of transcriptional regulators with ICEBERG [Preprint]. Genomics. <a href="https://doi.org/10.1101/2023.06.29.547050" rel="nofollow" target="_blank">https://doi.org/10.1101/2023.06.29.547050</a> </li> </ul> Related Episodes <ul><li> <a href="https://www.activemotif.com/podcasts#steven-henikoff" rel="nofollow" target="_blank">Chromatin Profiling: From ChIP to CUT&amp;RUN, CUT&amp;Tag and CUTAC (Steven Henikoff)</a> </li> <li> <a href="https://www.activemotif.com/podcasts#tim-petros" rel="nofollow" target="_blank">Single Cell Epigenomics in Neuronal Development (Tim Petros)</a> </li> </ul> Contact <ul><li> <ul><li> <a href="https://twitter.com/epigenetics_pod" rel="nofollow" target="_blank">Epigenetics Podcast on Twitter</a> </li> <li> <a href="https://www.instagram.com/epigenetics_pod/" rel="nofollow" target="_blank">Epigenetics Podcast on Instagram</a> </li> <li> <a href="https://podcasts.social/@epigenetics_pod" rel="nofollow" target="_blank">Epigenetics Podcast on Mastodon</a> </li> <li> <a href="https://twitter.com/activemotif" rel="nofollow" target="_blank">Active Motif on Twitter</a> </li> <li> <a href="https://www.linkedin.com/company-beta/35651/" rel="nofollow" target="_blank">Active Motif on LinkedIn</a> </li> <li> Email: <a href="mailto:podcast@activemotif.com">podcast@activemotif.com</a> </li> </ul> </li></ul>