Genome-wide data analysis

The dataset with accession [{"type":"entrez-geo","attrs":{"text":"GSE79222","term_id":"79222"}}GSE79222] was used for the ChIP-seq analysis (40). Paired-end data was aligned using Bowtie2 (v2.5.0) with default settings (41). The generated SAM files were sorted using SAMtools (V1.9) (42). Duplicate reads were then removed using the RmDup function of SAMtools. Coverage analysis was performed with the bamCoverage function from deepTools (v3.5.2) (43), with a specified bin size of 1 and normalization method set to CPM (Counts Per Million). Two replicate bigwig files were produced from the coverage analysis. These were combined using the bigwigCompare function to produce a mean ChIP file plotted.

The dataset with accession [{"type":"entrez-geo","attrs":{"text":"GSE159870","term_id":"159870"}}GSE159870] was used for the DRIPc-seq analysis (12). We used Wild Type G1-DRIPc-seq data. Reads were aligned to the Saccharomyces cerevisiae reference genome (sacCer3) using Rsubread (V2.0.1) software with the unique = TRUE option (44). The generated SAM files were sorted using SAMtools (V1.10) (42). Duplicate reads were then removed using the RmDup function of SAMtools. Reads were assigned to Watson or Crick strands with SAMtools. Coverage analysis was performed using the bamCoverage function from deepTools (v3.5.2) (43), with a specified bin size of 10 and normalization method set to RPKM. DRIPc-seq peak calling was performed using ChromstaR V1.12.0 with pre-set false discovery rate parameters (45).

Heatmaps were generated using the deeptools package (46), while Genome examples were plotted using IGV (v2.16.2) and sacCer3 features.

We utilized the public servers of usegalaxy.eu in conjunction with our in-house resources to execute all computational analyses previously described.