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/10.1101/866426v1

本数据集关联于我们题为《自然感受态流感嗜血杆菌摄取DNA的全基因组分析》的研究论文。该研究创新性地应用深度测序技术，定量检测流感嗜血杆菌摄取基因组片段的过程。本次附带的原始测序文件为fastq格式数据，其样本来源于经剪切为两种片段长度分布的86-028NP与PittGG菌株流感嗜血杆菌基因组DNA，且取自感受态流感嗜血杆菌Rd KW20的回收产物。本研究利用该数据构建了DNA摄取的基因组图谱，并将其与通过计算模型预测得到的DNA摄取量进行对比。通过该对比分析，我们进一步明晰了影响DNA片段摄取效率差异的关键因素。流感嗜血杆菌的DNA摄取过程，依赖于摄取复合物结合至一段被命名为USS的短DNA序列。本研究证实，摄取效率存在显著差异的基因组区域，其对应的USS序列具有截然不同的DNA空间构象，这提示空间构象可能在DNA结合过程中发挥重要作用。本论文的预印本可通过以下链接获取：https://www.biorxiv.org/content/10.1101/866426v1