Journal: bioRxiv

Article Title: Combined direct/indirect detection allows identification of DNA termini in diverse sequencing datasets and supports a multiple-initiation-site model for HIV plus-strand synthesis

doi: 10.1101/2023.06.12.544617

Figure Lengend Snippet: Fragmentation and sequencing of a genome with a , blocked termini and c , available termini. Resulting end capture, k -mer coverage, and strand bias for the case of b , blocked ends and d , available ends. b and d , Genome depicted with termini regions highlighted in gold and blue. Plots show coverage of sense (pink) and antisense (purple) DNA sequencing read starts, k -mer coverage for plus (blue) and minus (green) strand and calculated strand bias (red). d , Sequencing reads (blue arrows) captured from unblocked ends yield consistent 5’ and 3’ ends (black ovals) that are enriched in coverage. Here, strand bias is defined as + Coverage/– Coverage.

Article Snippet: Sequencing was performed using a tagmentase-based DNA fragmentation method (Nextera).

Techniques: Sequencing, DNA Sequencing

Journal: bioRxiv

Article Title: Combined direct/indirect detection allows identification of DNA termini in diverse sequencing datasets and supports a multiple-initiation-site model for HIV plus-strand synthesis

doi: 10.1101/2023.06.12.544617

Figure Lengend Snippet: The dataset (SRR3536210) , was obtained using a library prepared using DNA fragmentation and careful size selection. The precise size selection combined with severe drops in coverage at several points leads to an offset between sense and antisense coverage and hence to dramatic peaks in the strand bias plot, which would seem unlikely to correspond to true ends. shows an additional example, a case of a characterized linear genome ( C. reinhardtii mitochondrial genome). In the case of this dataset, the local coverage is uniform for much of the genome, suggesting that termini might indeed be evident in further analysis of the underlying sequence data. However, the presence of inverted terminal repeats on the linear molecule leads to complexities in counting coverage in the relevant regions. Anomalous strand ratios are observable in the terminal repeat regions, but the conflation of k -mers from left and right end repeats (due to the inverted nature of the repeats) makes a clear definition of the linear structure difficult.

Article Snippet: Sequencing was performed using a tagmentase-based DNA fragmentation method (Nextera).

Techniques: Selection, Sequencing

Journal: Frontiers in Microbiology

Article Title: Current strategies for mobilome research

doi: 10.3389/fmicb.2014.00750

Figure Lengend Snippet: Routes for analyzing plasmid diversity in recent publications.

Article Snippet: Previously, this was not feasible because of input DNA quantity requirements to sequencing library construction, but with the emergence of enzyme-based DNA fragmentation, such as Nextera XT®, as little as 20pg DNA can be used as input, theoretically allowing the omission of MDA ( ).

Techniques: Plasmid Preparation, DNA Purification, Amplification, Sequencing, Alkaline Lysis, Transformation Assay, Chromosome Walking, Filtration, Inverse PCR, Homogenization, Centrifugation, Sedimentation, In Silico