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2025
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| Online Access: | https://doi.org/10.5281/zenodo.14727323 |
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| author | N.G Martin, Hugo |
| author_facet | N.G Martin, Hugo |
| contents | <p><span>Pre-processed CUT&RUN files for P300 were normalized to effective genome size.</span><span><br><span><span>For each file, background signal was calculated in heterochromatin regions using negative</span></span><br><span><span>ATAC-seq signal mask, and subsequently removed from the overall coverage. </span></span></span></p> <p><span>Peak calling on each replicate was performed using MACS252 v.2.2.7.1, and the</span><span><br><span><span>consensus overlapping peaks between all replicates were considered as reproducible for the</span></span><br><span><span>corresponding dataset. Number of overlapping peaks between conditions was calculated in R</span></span><br><span><span>with subsetByOverlaps (GenomicRanges v.1.54.1)57, and nearest genes were annotated to</span></span><br><span><span>peaks using biomaRt.</span> Promoter regions of those genes (± 1kb TSS) were extracted using the Rsubread</span></span> <span>v.2.16.0) package, and the CUT&RUN signal was quantified with multiBigwigSummary from</span> <span>deepTools package</span>.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_14727323 |
| institution | Zenodo |
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| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Cut&RUN P300 BA Primary mouse hepatocytes N.G Martin, Hugo <p><span>Pre-processed CUT&RUN files for P300 were normalized to effective genome size.</span><span><br><span><span>For each file, background signal was calculated in heterochromatin regions using negative</span></span><br><span><span>ATAC-seq signal mask, and subsequently removed from the overall coverage. </span></span></span></p> <p><span>Peak calling on each replicate was performed using MACS252 v.2.2.7.1, and the</span><span><br><span><span>consensus overlapping peaks between all replicates were considered as reproducible for the</span></span><br><span><span>corresponding dataset. Number of overlapping peaks between conditions was calculated in R</span></span><br><span><span>with subsetByOverlaps (GenomicRanges v.1.54.1)57, and nearest genes were annotated to</span></span><br><span><span>peaks using biomaRt.</span> Promoter regions of those genes (± 1kb TSS) were extracted using the Rsubread</span></span> <span>v.2.16.0) package, and the CUT&RUN signal was quantified with multiBigwigSummary from</span> <span>deepTools package</span>.</p> |
| title | Cut&RUN P300 BA Primary mouse hepatocytes |
| url | https://doi.org/10.5281/zenodo.14727323 |