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

LongTREC：长读长转录组学欧洲联盟。

• 批准号: EP/X035913/1
• 负责人: Wilfried Haerty
• 金额: $ 33.8万
• 依托单位: Earlham Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2022
• 资助国家: 英国
• 起止时间: 2022 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=EP%2FX035913%2F1
• 关键词: LongTREC; Long; Reads; Transcriptomics; European

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.

第三代单分子长读测序技术，如Nanopore和PacBio，正在给转录组研究带来革命性的变化，并有望在基因表达研究方面击败短读测序。然而，要实现这一全部潜力，存在着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，成为欧洲和世界长阅读转录组测序(LrRNA-seq)领域的领导者。该团队将解决这些技术目前面临的进步障碍的三个基本方面。A)通过改进的文库制备协议和生物信息学前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，将这些方法应用于大批量和单细胞样本的基因组注释和异构体使用分析，以及c)将长阅读扩展到用于调控生物学研究的多组学应用。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，包括与紧迫的社会挑战有关的活动，如气候变化、多样性和包容性以及科学伦理。学生将通过借调到欧洲顶尖实验室和公司以及接触到RNA研究领域的全球专家网络来补充他们的教育。

项目成果

Single-cell gene and isoform expression analysis reveals signatures of ageing in haematopoietic stem and progenitor cells.

• DOI: 10.1038/s42003-023-04936-6
• 发表时间: 2023-05-24
• 期刊: COMMUNICATIONS BIOLOGY
• 影响因子: 5.9
• 作者: Mincarelli, Laura;Uzun, Vladimir;Wright, David;Scoones, Anita;Rushworth, Stuart A.;Haerty, Wilfried;Macaulay, Iain C.
• 通讯作者: Macaulay, Iain C.

U6 snRNA m6A modification is required for accurate and efficient cis- and trans-splicing of C. elegans mRNAs.

U6 snRNA m6A 修饰是线虫 mRNA 准确有效的顺式和反式剪接所必需的。

• DOI: 10.1101/2023.09.16.558044
• 发表时间: 2023
• 期刊: bioRxiv : the preprint server for biology
• 作者: Shen,Aykut;Hencel,Katarzyna;Parker,MatthewT;Scott,Robyn;Skukan,Roberta;Adesina,AduragbemiS;Metheringham,CareyL;Miska,EricA;Nam,Yunsun;Haerty,Wilfried;Simpson,GordonG;Akay,Alper
• 通讯作者: Akay,Alper

Schizosaccharomyces versatilis represents a distinct evolutionary lineage

多功能裂殖酵母代表了独特的进化谱系

• DOI: 10.1101/2023.09.04.556188
• 发表时间: 2023
• 作者: Etherington G