Two readers for RNA

两个 RNA 阅读器

• 批准号: 10428680
• 负责人: Anna Schibel
• 金额: $ 39.4万
• 依托单位: ELECTRONIC BIOSCIENCES, INC.
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-07-20 至 2024-03-19
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10428680
• 关键词: Benchmarking; Biological; Biological Sciences; ChIP-seq; Church; Complementary DNA; Computer software; DNA; DNA Sequence; Data; Detection; Development; Diagnostic; Ensure; Enzymes; Evaluation; Future; Generations; Genomics; Goals; Gold; Image; Individual; Intervention; Investigation; Label; Lead; Length; Libraries; Lipid Bilayers; Longevity; Magnetism; Measurement; Methodology; Methods; Modification; Motion; Motivation; Motor; Nucleotides; Phase; Polymers; Positioning Attribute; Preparation; RNA; Reader; Regulation; Research; Resolution; Reverse Transcription; Running; Sampling; Small Business Innovation Research Grant; Speed; Stretching; System; Systems Integration; Technology; Therapeutic Intervention; Third Generation Sequencing; Time; Validation; War; base; clinically relevant; cost; ds-DNA; epigenomics; epitranscriptome; epitranscriptomics; improved; instrumentation; magnetic field; nanopore; novel; particle; prognostic; programs; prototype; sequencing platform; single molecule; solid state; technology development; transcriptome; transcriptome sequencing; transcriptomics; voltage

Project Summary Nanopore-based technology has the potential to be the future of comprehensive RNA sequencing, i.e., transcriptomics and epitranscriptomics, as it is the only viable path to directly characterizing and profiling long RNA strands without reverse transcription or processive enzymes that fail to traverse certain sequences. The direct characterization enabled by nanopore sequencing will also ultimately lead to detection and characterization of modified bases, a critical requirement for epitranscriptomics. The presently available, state- of-the art RNA sequencing technologies are limited by the method, with the input requiring cDNA intermediates and/or large amounts of costly sample, and the readout featuring a compromise between short read length and low-accuracy. During this program, Electronic BioSciences (EBS) aims to develop a completely new long-read, extremely high-accuracy nanopore-based sequencing technology that will enable de novo epitranscriptomic sequencing, capable of inherent sequence cross-validation and expanded sensitivity for more accurate and versatile RNA sequencing. During this Phase I project, we will build and multiplex an entirely new system, fully assess and optimize the associated workflow/methodology to sequence canonical nucleotides and specific clinically relevant RNA modifications, and demonstrate initial sequencing. At the conclusion of this project, we will have successfully demonstrated and developed an entirely new sequencing system prototype that overcomes the known challenges limiting current RNA sequencing technologies (including other nanopore- based sequencing approaches). The resulting technology development will be a label-free, long-read (>kbases), electronic readout method, capable of providing a new and detailed understanding of RNA and its regulation.

项目摘要 基于纳米孔的技术有可能成为综合RNA测序的未来，即， 转录和表位转录组学，因为这是直接描述和剖析Long的唯一可行的途径 没有逆转录或不能穿越特定序列的过程酶的RNA链。这个 通过纳米孔测序实现的直接表征最终也将导致检测和 修饰碱基的表征，这是表位转录组学的关键要求。目前可用的，述明- Of-art rna测序技术受到该方法的限制，输入需要cdna中间体。 和/或大量昂贵的样本，并且读出的特征是在短读取长度和 精确度低。在这个项目中，电子生物科学(EBS)的目标是开发一种全新的长期阅读， 极高精度的基于纳米孔的测序技术，将使从头开始的表位转录 测序，能够固有的序列交叉验证和扩展的敏感性，以实现更准确和 多用途的RNA测序。在这个第一阶段的项目中，我们将建造和多路传输一个全新的系统，完全 评估和优化相关的工作流程/方法，以测序标准核苷酸和特定的 临床相关的RNA修饰，并演示了初始测序。在这个项目结束时，我们 将成功演示和开发一种全新的测序系统原型 克服了限制当前RNA测序技术的已知挑战(包括其他纳米孔- 基于测序方法)。由此产生的技术开发将是一种无标签、长时间阅读(&gt；kbase)、 电子读数方法，能够提供对RNA及其调控的新的和详细的理解。