DOI: 10.5281/zenodo.2632998
title: Experimental data and benchmarks used in the paper "Nucleosome Dynamics: A new tool for the dynamic analysis of nucleosome positioning"

description: Experimental data used to illustrate the analysis with Nucleosome Dynamics pipeline. Three publicly available data sets were used: Yeast metabolic cycle MNase-seq data downloaded from GEO under accession number GSE77631 corresponding to time points 9 and 12<br> Nocetti, N., and Whitehouse, I. (2016). Nucleosome repositioning underlies dynamic gene expression. Genes & Development 30, 660–672. MNase-seq data for S. cerevisiae cells synchronized in G1 and S phase, as described by Deniz (2016). Raw data available under accession number SAMEA2698380<br> Deniz, Ö., Flores, O., Aldea, M., Soler-López, M., and Orozco, M. (2016). Nucleosome architecture throughout the cell cycle. Scientific Reports 6, 19729. MNase-seq data for S. cerevisiae grown in different media: YPD, Gal, and EtOH. Data aligned to sacCer1 downloaded from GEO using accession numbers GSM351492, GSM351493, and GSM351494. Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ et al. The DNA-encoded nucleosome organization of a eukaryotic genome. <em>Nature</em> 2009 Mar 19;458(7236):362-6. PMID: 19092803 Each tar file contains two folders: inputs: bam/RData files can be used to run Nucleosome Dynamics analyses. bigWig files contain nucleosome coverage and can be used to visualise in a genome browser. outputs: results from all analyses (nucleR, NFR, TSS, Periodicity, Stiffness, NucDyn) Simulated data used to benchmark nucleosome positioning by nucleR, and nucleosome dynamics by NucDyn, DANPOS and Dimnp. <strong>Figure </strong><strong>2B: </strong>synthetic data simulated for comparison of nucleR and Danpos to detect a second family of nucleosomes. Each folder pX contains simulations when the second nucleosome is present in X% of the families. <strong>Figure 2C</strong>: Distance between the dyads identified by nucleR and DANPOS to the dyad position in the true synthetic nucleosome map for fuzzy and well positioned nucleosomes. <strong>Figure 2D</strong>: Synthetic data used to compute sensitivity of the EVICTION prediction for NucDyn, DANPOS and Dimnp. Evictions were simulated removing reads from a given percentage of families (10%, 20%, …, 90%) and were identified from DANPOS output as a nucleosome with point_log2FC &lt; -1 and point_diff_FDR &lt; 0.01 (point with highest difference in the two samples, as reported by the software), and with default parameters for Dimnp <strong>Figure 2E</strong>: Synthetic data used to compute sensitivity of the SHIFT prediction. Shifts were introduced displacing reads from 1 to 5 DNA turns (i.e. 10-50 bp) and modifying different percentages of the families (10%, 20%, …, 90%). For each simulated data: <em> *.RData</em> files can be used to run nucleR or NucDyn (*mod* corresponds to the modified reads: eviction or shift introduced) <em>*.bed </em>files can be used to run DANPOS or Dimnp (*mod* corresponds to the modified reads: eviction introduced) results/ folder contains results from DANPOS <em>NR.gff</em> contains the results from nucleR (*mod* corresponds to the results for modified reads: eviction or shift introduced) <em>ND.gff</em> contains the results from NucDyn <em>res_dimnp_*</em> contains the results from Dimnp <strong>FigSupDanposShift:</strong> Synthetic data used to compute sensitivity of the SHIFT prediction for DANPOS. Shifts were introduced displacing reads from 1 to 5 DNA turns (i.e. 10-50 bp) and modifying different percentages of the families (10%, 20%, …, 90%) and were identified from DANPOS output as a nucleosome with treat2control_dis-10 larger than the given displacement and point_diff_FDR &lt; 0.01 (point with highest difference in the two samples, as reported by the software). For each simulated data: <em> *.bed</em> files contain the modified nucleosome positions <em>results</em> folder contains output from DANPOS