DanioPeaks: A Central Resource for Standardised Annotation and Re-annotation of Whole-Genome Data for the Model Vertebrate Zebrafish

DanioPeaks：模型脊椎动物斑马鱼全基因组数据标准化注释和重新注释的中心资源

• 批准号: BB/N023358/1
• 负责人: Boris Lenhard
• 金额: $ 17.83万
• 依托单位: Imperial College London
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2017
• 资助国家: 英国
• 起止时间: 2017 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FN023358%2F1
• 关键词: DanioPeaks; Central; Resource; Standardised; Annotation

We address the scientific demand that stems from recent developments in high-throughput genomics, including the landmark ENCODE project and the new 100K genomes project (UK): the need for a suitable vertebrate model that enables high-throughput in vivo functional testing of hypotheses generated from genome-scale annotation projects. With its abundantly available, transparent and externally developing embryos and larvae, large biomass that is crucial for high-throughput methods, fast assays of gene loss of function, a reference genome sequence, and thousands of genetic mutants, zebrafish is one of the best models for studying the structure and function of genomes in vertebrate development and disease. However, zebrafish will not be able to fulfill its potential unless its genome is comprehensively annotated for functional coding and non-coding elements, similarly to human and mouse. DanioPeaks addresses this problem by developing a bioinformatic annotation and re-annotation pipeline and providing a genomics resource for the wider genomics community. DanioPeaks aims to develop the processing pipeline for analysis of all published NGS sequencing datasets (over ten thousand NGS sequencing datasets) available for zebrafish by using established standardised protocols of ENCODE and modENCODE. It will provide the means to secure the computational power and analysis tools for remapping and reanalysing up to 16.2 TB of NGS experiment data to the most recent (final) version of the zebrafish genome sequence and to make these data comparable and available for metaanalysis to the wider scientific community. DanioPeaks will collect all zebrafish NGS raw data to a single database by upload using the zebrafish Data Coordination Centre. Raw data will be processed by ENCODE processing pipeline and mapped to GRZc10 genome assembly. Secondary analysis for feature/peak calling will be carried out and submitted to ZFIN-based track hub for visualisation in gene browsers (e.g. Ensembl). The outcome will be a community repository, a publicly accessible epigenome resource and a multicenter genome resource paper with new biology identified from the reanalyzed zebrafish data in a major genomics journal.

我们解决了高通量基因组学最近发展的科学需求，包括具有里程碑意义的ENCODE项目和新的100K基因组项目（英国）：需要一个合适的脊椎动物模型，能够对基因组规模注释项目产生的假设进行高通量体内功能测试。斑马鱼拥有丰富的、透明的和外部发育的胚胎和幼虫，巨大的生物量对高通量方法至关重要，基因功能丧失的快速测定，参考基因组序列和数千个基因突变，是研究脊椎动物发育和疾病中基因组结构和功能的最佳模型之一。然而，除非像人类和小鼠一样，对斑马鱼的基因组进行功能编码和非编码元素的全面注释，否则斑马鱼将无法发挥其潜力。DanioPeaks通过开发生物信息学注释和再注释管道来解决这个问题，并为更广泛的基因组学社区提供基因组学资源。DanioPeaks的目标是开发处理管道，通过使用ENCODE和modENCODE的标准化协议，分析所有已发表的可用于斑马鱼的NGS测序数据集（超过10,000个NGS测序数据集）。它将提供确保计算能力和分析工具的手段，以将高达16.2 TB的NGS实验数据重新映射和重新分析为最新（最终）版本的斑马鱼基因组序列，并使这些数据具有可比性，并可用于更广泛的科学界的荟萃分析。DanioPeaks将通过使用斑马鱼数据协调中心上传，将所有斑马鱼NGS原始数据收集到一个数据库中。原始数据经过ENCODE处理流水线处理，映射到GRZc10基因组组装。将对特征/峰值调用进行二次分析，并将其提交到基于zfin的track hub，以便在基因浏览器（例如Ensembl）中进行可视化。结果将是一个社区存储库，一个公开访问的表观基因组资源和一篇多中心基因组资源论文，其中从重新分析的斑马鱼数据中确定了新的生物学，并发表在主要的基因组学期刊上。

项目成果

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.

• DOI: 10.1038/s41588-022-01089-w
• 发表时间: 2022-07
• 期刊: NATURE GENETICS
• 影响因子: 30.8
• 作者: Baranasic, Damir;Hortenhuber, Matthias;Balwierz, Piotr J.;Zehnder, Tobias;Mukarram, Abdul Kadir;Nepal, Chirag;Varnai, Csilla;Hadzhiev, Yavor;Jimenez-Gonzalez, Ada;Li, Nan;Wragg, Joseph;D'Orazio, Fabio M.;Relic, Dorde;Pachkov, Mikhail;Diaz, Noelia;Hernandez-Rodriguez, Benjamin;Chen, Zelin;Stoiber, Marcus;Dong, Michael;Stevens, Irene;Ross, Samuel E.;Eagle, Anne;Martin, Ryan;Obasaju, Oluwapelumi;Rastegar, Sepand;McGarvey, Alison C.;Kopp, Wolfgang;Chambers, Emily;Wang, Dennis;Kim, Hyejeong R.;Acemel, Rafael D.;Naranjo, Silvia;Lapinski, Maciej;Chong, Vanessa;Mathavan, Sinnakaruppan;Peers, Bernard;Sauka-Spengler, Tatjana;Vingron, Martin;Carninci, Piero;Ohler, Uwe;Lacadie, Scott Allen;Burgess, Shawn M.;Winata, Cecilia;van Eeden, Freek;Vaquerizas, Juan M.;Luis Gomez-Skarmeta, Jose;Onichtchouk, Daria;Brown, Ben James;Bogdanovic, Ozren;van Nimwegen, Erik;Westerfield, Monte;Wardle, Fiona C.;Daub, Carsten O.;Lenhard, Boris;Muller, Ferenc
• 通讯作者: Muller, Ferenc

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.

• DOI: 10.1093/nar/gkx1188
• 发表时间: 2018-01-04
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Khan A;Fornes O;Stigliani A;Gheorghe M;Castro-Mondragon JA;van der Lee R;Bessy A;Chèneby J;Kulkarni SR;Tan G;Baranasic D;Arenillas DJ;Sandelin A;Vandepoele K;Lenhard B;Ballester B;Wasserman WW;Parcy F;Mathelier A
• 通讯作者: Mathelier A