Efficient and reliable shearing of chromatin for high-throughput analysis

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- This application is to finance an immediate and urgent need for reliably and reproducibly shearing DNA for protocols such as Chromatin immunoprecipitation (ChIP) and Chromatin RNA immunoprecipitation (ChRIP). These techniques identify Protein-DNA and RNA-Protein-DNA interactions, respectively, and require a sonication (chromatin shearing) step that is critical for the success of the experiments. The requested equipment is a Covaris ME220 Focused-ultrasonicator that will facilitate the study of many aspects of these interactions at the chromatin level. The four applicants on this application possess complementary expertise and use a broad range of biological systems to address these critical questions. They focus on answering biological questions regarding: 1) cell state stabilization by transcription factors and non-coding RNAs (team Hussein), 2) the dynamics between DNA damage/repair and chromatin (team Fradet-Turcotte), 3) chromosome architecture and transcriptional regulation (team Bilodeau), and 4) the biogenesis and epigenetic regulation of ribosomal RNAs (team Moss).***The Covaris ME220 focused-ultrasonicator provides several characteristics that will improve the reliability and quality of our results and meet much of our needs. It overcomes many of the technical and practical issues that are raised due to unreliable and inconsistent results produced by outdated sonicators, and sample and volume limitations. The ME220 focused-ultrasonicator provides reproducible results due to its high-performance sample preparation and Adaptive Focused Acoustics design. This feature prevents heat induced sample damage, which can cause bias and variation between experiments. It allows using 8 samples simultaneously with an add-on option to upgrade to 96 samples. This option increases the versatility and high-throughput capacity of the sonicator, which is not found in other sonicators. It can use volumes as low as 15µL, which is an extremely important feature, when using precious samples or samples with very low cell numbers. Furthermore, the ME220 focused-ultrasonicator is a user-friendly and well-designed system with preloaded protocols that enable training of HQP from all levels of experience. Overall, the ME220 focused-ultrasonicator outperforms many available sonicators on the market and will replace our outdated system. Moreover, it will increase our competitiveness and our ability to produce highly skilled HQP for the academic as well as industrial job market.*****