Genome-wide analysis of DNA uptake by naturally competent Haemophilus influenzae

This is the data associated with our paper "Genome-wide analysis of DNA uptake by naturally competent Haemophilus influenzae". The paper used an innovative application of deep sequencing to measure how Haemophilus influenzae takes up genomic fragments. Files attached are the raw sequencing files in fastq formoat of the sequenced Haemophilus influenzae genomic DNA from 86-028NP and PittGG strains sheared into two size distributions and recovered from competent H. influenzae Rd KW20. We used this data to built genomic maps of DNA uptake, which were compared to our predicted uptake calculated using a computational model. This comparison allowed us to increase our understanding of factors explaining differences in uptake of DNA fragments. DNA uptake in Haemophilus influenzae depends on the uptake machinery binding to a short DNA sequence denominated "USS". Our paper was able to show that genomic regions with high and low uptake had USS with distinct DNA-shape, suggesting that shape might have a role in DNA-binding. Preprint of the paper can be found in the link below: https://www.biorxiv.org/content/10.1101/866426v