LongTREC: The Long-Reads Transcriptomics European Consortium. The next generation transcriptome biology revealed by single molecule seq. technologies

第三代单分子长读段测序技术（如Nanopore和Pacbio）正在彻底改变转录组研究，并有望在基因表达研究中击败短读段测序。然而，要充分实现这一潜力，还存在技术和生物信息学方面的挑战。在这个项目中，我们将培养一支优秀的早期研究人员团队，成为欧洲和世界长读段转录组测序（lrRNA-seq）领域的领导者。该团队将解决这些技术所面临的当前进展障碍的三个基本方面。a）从改进的文库制备方案和生物信息学预处理方法获得高质量的测序和预处理数据，B）建立基准分析管道，用于将这些方法应用于批量和单细胞样品中的基因组注释和同种型使用分析，以及c）将长读段扩展到多组学应用，用于调控生物学的研究。此外，ERS将遵循由科学和软技能培训组成的密集和全面的培训计划，包括与气候变化，多样性和包容性以及科学伦理等紧迫社会挑战相关的活动。学生将通过借调到欧洲顶级实验室和公司以及通过接触RNA研究领域的全球专家网络来补充他们的教育。

Third-generation, single-molecule long-read sequencing technologies such as Nanopore and Pacbio are revolutionizing transcriptome research and are expected to outcompete short-reads sequencing for gene expression studies. However, technical and bioinformatics challenges exist to the realization of this full potential. In this project, we will train a team of excellent Early Stage Researchers to become the European and world leaders in the field of long reads transcriptome sequencing (lrRNA-seq). The team will address three fundamental aspects of current barriers to the progress that these technologies face. a) Obtaining high-quality sequencing and preprocessed data from improved library preparation protocols and bioinformatics preprocessing methods, b) Establishment of benchmarked analysis pipelines for the application of these approaches to genome annotation and isoform usage analysis both in bulk and single-cell samples, and c) Extension of long reads to multi-omics applications for the study of regulatory biology. Additionally, ERS will follow an intensive and comprehensive training program composed of scientific and soft skills training, including activities related to pressing societal challenges such as climate change, diversity and inclusion, and the ethics of science. Students will complement their education through secondments in top European laboratories and Companies as well as through exposure to a network of worldwide experts in the field of RNA research.