Experimental data and benchmarks used in the paper "Nucleosome Dynamics: A new tool for the dynamic analysis of nucleosome positioning"

Experimental data used to illustrate the analysis with Nucleosome Dynamics pipeline. Three publicly available data sets were used:

1. Yeast metabolic cycle MNase-seq data downloaded from GEO under accession number GSE77631 corresponding to time points 9 and 12
   Nocetti, N., and Whitehouse, I. (2016). Nucleosome repositioning underlies dynamic gene expression. Genes & Development 30, 660–672.

2. 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
   Deniz, Ö., Flores, O., Aldea, M., Soler-López, M., and Orozco, M. (2016). Nucleosome architecture throughout the cell cycle. Scientific Reports 6, 19729.

3. 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. Nature 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.

Figure 2B: 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.

Figure 2C: 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.

Figure 2D: 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 < -1 and point_diff_FDR < 0.01 (point with highest difference in the two samples, as reported by the software), and with default parameters for Dimnp 

Figure 2E: 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:

•  *.RData files can be used to run nucleR or NucDyn (*mod* corresponds to the modified reads: eviction or shift introduced)
• *.bed files can be used to run DANPOS or Dimnp  (*mod* corresponds to the modified reads: eviction introduced)
• results/ folder contains results from DANPOS
• NR.gff contains the results from nucleR (*mod* corresponds to the results for modified reads: eviction or shift introduced)
• ND.gff contains the results from NucDyn
• res_dimnp_* contains the results from Dimnp

FigSupDanposShift: 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 < 0.01 (point with highest difference in the two samples, as reported by the software).

For each simulated data:

•  *.bed files contain the modified nucleosome positions
• results folder contains output from DANPOS