Genomic DNA and Hi-C sequencing of 14 representative bacterial strains with large extrachromosomal replicons

This dataset was generated to investigate how large extrachromosomal replicons (ERs) integrate into bacterial replication and segregation systems. These ERs, sometimes nearly the size of the main chromosome, are widespread among bacteria, yet their behavior during the cell cycle remains poorly understood. The goal of this study was to explore their replication timing and spatial organization within the cell.

The dataset contains paired-end FastQ files from genomic DNA and Hi-C sequencing of 14 bacterial strains harboring large ERs. Strains include representatives from Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deinococci, and Spirochaetes.

The dataset is organized into one folder per bacterial strain. Each folder contains:

(1) FastQ files from Hi-C sequencing. Hi-C is a chromosome conformation capture technique performed on exponentially growing cells. It reveals physical interactions between different genomic regions, including contacts between chromosomes and ERs, providing insights into their spatial organization.

(2) FastQ files from genomic DNA sequencing. Genomic DNA was extracted from exponential and stationary phase cultures and used for Marker Frequency Analysis (MFA). MFA estimates replication dynamics by analyzing read coverage along the genome, enabling identification of replication origins and termini, as well as estimation of replication fork speed and the relative timing of initiation and termination between replicons.