PIXUL^® Multi-Sample Sonicator

Extremely Consistent Shearing of Genomic DNA

Highly consistent shearing of genomic DNA to an appropriate size for conversion into functional NGS libraries is integral to high quality and comparable next-generation sequencing data. Manual shearing with a probe sonicator or shearing with an inconsistent high-throughput sonicator can lead to sample-to-sample variability.

To test the consistency of the PIXUL Multi-Sample Sonicator, purified genomic DNA was loaded into all 96 wells of the PIXUL 96-well plate, processed, and fragmentation profiles examined for sonication consistency and efficiency. Highly consistent average fragment lengths and standard deviations were observed across the entire plate.

For consistent gDNA shearing, we recommend the PIXUL gDNA Shearing Kit.

Figure 1: The PIXUL Multi-Sample Sonicator consistently sonicates purified genomic DNA samples to an optimal fragmentation profile. 10 µg of salmon sperm DNA was loaded into each well of the PIXUL 96-well plate. The samples were processed for 36 minutes. Fragmentation profiles were examined on an agarose gel. Average fragment size is 307 +/- 35 bp. Nucleic Acids Res. 2019 Jul 9; 47(12):e69.

PIXUL Delivers More Consistent Chromatin Shearing than Competitor C

ChIP-Seq studies benefit from relatively narrow and consistent chromatin shearing profiles, as this can improve the resolution of transcription factor binding sites or the locations of histone post-translational modifications.

To evaluate chromatin sonication consistency between different multi-sample sonicators, we compared chromatin shearing performed with the PIXUL to a leading Competitor C sonication system. PIXUL demonstrated more consistency in chromatin shearing than the Competitor C system.

For consistent chromatin shearing, we recommend the PIXUL Chromatin Shearing Kit. The Chromatin Input Preparation Kit makes it easy to quantitate yield and fragmentation efficiency prior to ChIP.

Figure 2: The PIXUL Multi-Sample Sonicator consistently sonicates chromatin to an optimal fragmentation profile. 200,000 HCT116 cells were loaded into each well of the PIXUL 96-well plate or the proprietary Competitor C plate. Sonication of these samples was performed and fragmentation profiles were examined by agarose gel electrophoresis. PIXUL samples have a tighter size distribution and increased consistency across the plate. Nucleic Acids Res. 2019 Jul 9; 47(12):e69.

PIXUL Enables More Consistent Sonication and Higher Chromatin Recovery than Competitor D

ChIP-Seq studies have historically required chromatin preparation from millions of cells because the limitations created by inefficienct sonication. As ChIP-Seq techniques have progressed, the number of input cells required has decreased by maximizing the efficiency of sonication and chromatin recovery.

PIXUL 96-well plates are compatible with cell culture, fixation, and sonication steps there's no need to transfer samples from culture plates to sonication plates and risk sample loss. Compared to Competitor D, PIXUL exhibits a tighter size distribution of chromatin fragments following sonication, as well as higher chromatin recovery (data not shown).

Figure 3: The PIXUL Multi-Sample Sonicator consistently sonicates chromatin to an optimal fragmentation profile. HEK293 cells were loaded into each well of the PIXUL 96-well plate. They were cultured, fixed, and chromatin fragmented in the same plate without any sample transfers. Competitor D exhibits less consistent fragmentation. Nucleic Acids Res. 2019 Jul 9; 47(12):e69.

PIXUL Delivers Equivalent Exome Sequencing Results as Competitor C for a Fraction of the Cost

PIXUL was compared to Competitor C in an exome sequencing experiment, which requires DNA shearing as a first step. Using 500 ng of input DNA, samples were sheared with either PIXUL or Competitor C, libraries were constructed, enriched for the exome, and sequenced. Several sequencing metrics were analyzed to determine the PIXUL instrument produced exome libraries that performed equivalently to Competitor C, at just a fraction of the sample preparation cost for the instrument and consumables. 

Figure 4: The PIXUL and Competitor C sonication systems were used to shear 500 ng genomic DNA samples prior to constructing exome sequencing libraries. NGS metrics indicate that these libraries performed equivalently. Nucleic Acids Res. 2019 Jul 9; 47(12):e69.