High-throughput RNA-Seq of clinical samples using Covaris AFA ultrasonication

RNA-Seq remains a critical and robust methodology in understanding cellular and organismal changes associated with development and disease. Advances in automation have helped reduce the cost of creating RNA-Seq libraries significantly. A key challenge for automation remains the variability of the quality of input material, particularly from clinical samples, that can require sample-by-sample modification of the protocols. To address this, we have used Covaris Adaptive Focused Acoustics (AFA) technology as an alternative to cations to standardize fragmentation of RNA in the first stage of library preparation. Sonication can be standardized for all samples, regardless of their initial integrity, to produce regular fragmented RNA suitable for rRNA depletion-based Illumina library preparation. This homogeneous treatment results in more reproducible libraries with minimal bias in the RNA-Seq data. AFA based RNA fragmentation is suitable for automated library preparation and workflow miniaturization, resulting in significant cost savings.

 

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