Journal: PLoS ONE
Article Title: Cavitation Enhancing Nanodroplets Mediate Efficient DNA Fragmentation in a Bench Top Ultrasonic Water Bath
Figure Lengend Snippet: Saccharomyces cerevisiae gDNA (BY4741) fragmented with nanodroplets in an ultrasonic water bath was comparable in quality to DNA fragmented in a commercially available device. (A) Agilent D1000 ScreenTape data showing size distribution of DNA fragmented in tubes without (left panel) or tubes with nanodroplets (right panel). Average size is indicated in base pairs (bp). DNA size markers are denoted by Upper and Lower. (B) False gel picture indicating that DNA fragmented without nanodroplets had an average fragment size > 1,500 bp. Purple bars indicate the upper (1,500 bp) molecular weight marker and green bars indicate the lower (25 bp) molecular weight marker in each lane. (C) Size distribution of DNA after sequencing library preparation. Average size is shown in base pairs (bp). DNA size markers are denoted by Upper and Lower. (D) Mapping sequencing reads to the Saccharomyces cerevisiae (S288c) reference genome is comparable in detection of single nucleotide variations and indels in Fig 4C . Abundance and profile of relative errors in sequencing reads does not indicate a difference in the presence of error bias in the data compared to data in Fig 4C .
Article Snippet: For high throughput sequencing preparation, each sample was concentrated in a Zymo Research ChIP DNA Clean & Concentrator column (Zymo Research, Irvine, CA, USA #D5201), followed by quantitation on a Qubit 2.0 Fluorometer. (Life Technologies, Grand Island, NY, USA) DNA fragment quality and size was assessed using an Agilent D1000 ScreenTape system (Agilent Technologies, Santa Clara, CA, USA).
Techniques: Molecular Weight, Marker, Sequencing