Analysis scripts and source data for Rpd3L regulates Transcription-Replication Conflict via H3K4 Methylation-Dependent and Independent Chromatin Mechanisms

This Zenodo record contains the first stable version (v1.0.0) of the analysis scripts and source data associated with the manuscript "Rpd3L regulates Transcription-Replication Conflict via H3K4 Methylation-Dependent and Independent Chromatin Mechanisms".

Overview
The deposited files include shell scripts for sequencing data processing and downstream analysis, BED files defining gene sets used for region-based analyses, per-gene signal tables generated from normalized BigWig files, source data used to generate quantitative figures, mutation rate raw data, and growth curve raw data.

Contents
- scripts.zip: Shell scripts used for read mapping, BAM processing, BigWig generation, signal quantification and PCA.
- gene_lists.zip: BED files defining gene sets used for region-based analyses.
- source_data.zip: Processed data tables and source data used to generate quantitative figures.
- per_gene_signal_tables.zip: Average normalized signal values for each gene or genomic region.
- mutation_rates.zip: Raw data used for mutation rate analyses.
- growth_curves.zip: Raw data used for growth curve analyses.

Usage
The analysis scripts are organized as independent shell scripts and can be reproduced in Bash after replacing placeholder paths and sample-specific file names with the appropriate input files.

Data availability
Raw sequencing reads are deposited separately in the NCBI Sequence Read Archive (SRA) under BioProject accession number PRJNA1399756. Processed sequencing data have been deposited in the NCBI Gene Expression Omnibus (GEO) under accession number GSE315970.