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.

项目概要 基于纳米孔的技术有潜力成为全面 RNA 测序的未来，即 转录组学和表观转录组学，因为它是直接表征和分析长片段的唯一可行途径 没有逆转录或进行酶的 RNA 链，无法遍历某些序列。这 通过纳米孔测序实现的直接表征也将最终导致检测和 修饰碱基的表征，这是表观转录组学的关键要求。目前可用的状态- 最先进的RNA测序技术受到方法的限制，输入需要cDNA中间体 和/或大量昂贵的样品，并且读数具有短读取长度和 低准确度。在此计划中，电子生物科学 (EBS) 旨在开发一种全新的长读、 极其高精度的基于纳米孔的测序技术，将使从头表观转录组学成为可能 测序，能够进行固有的序列交叉验证和扩展的灵敏度，以获得更准确和更准确的结果 多功能RNA测序。在第一阶段项目中，我们将构建和复用一个全新的系统，完全 评估和优化相关的工作流程/方法来对规范核苷酸和特定的序列进行测序 临床相关的 RNA 修饰，并展示初始测序。在这个项目结束时，我们 将成功展示并开发出一种全新的测序系统原型 克服了限制当前 RNA 测序技术（包括其他纳米孔测序技术）的已知挑战 基于测序的方法）。由此产生的技术开发将是无标签、长读（>kbases）、 电子读出方法，能够提供对 RNA 及其调控的新的、详细的理解。