APEXdb: A Comprehensive Dataset for APEX-Dependent RNA Proximity Biotinylation
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APEXdb is the first publicly available, curated dataset dedicated to APEX-dependent proximity biotinylation strategies. This resource serves as a centralized hub for researchers to explore protein-RNA interactions and evaluate the spatial transcriptome within various cellular contexts. Resource Overview PLANSdb aggregates and annotates all currently available data regarding RNAs identified as interactors or neighbors of specific APEX-tagged protein baits. By compiling disparate experimental results into a unified framework, you can: Search for specific protein-RNA interactions Assess the specificity of identified interactors Distinguish between promiscuous "background" RNAs and biologically significant specific interactions Data Composition and Metadata To ensure reproducibility and facilitate cross-study comparisons, every entry in PLANSdb is enriched with comprehensive experimental metadata, including: Bait Information: Type of tag used and its specific cellular localization Biological Context: Cell line utilized and the specific stress conditions applied during the experiment Technical Specifications: Type of starting material for sequencing and the sequencing platform adopted Integration and Future Growth PLANSdb is not a static resource. It integrates novel data generated within this project and is designed for continuous expansion. Our team will regularly incorporate new datasets as they are produced, ensuring that the community has access to the most up-to-date proximity labeling information available. At the moment data from the following published works is integrated: Padrón, Alejandro et al. “Proximity RNA Labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules.” Molecular cell vol. 75,4 (2019): 875-887.e5. doi:10.1016/j.molcel.2019.07.030 Barutcu, A Rasim et al. “Systematic mapping of nuclear domain-associated transcripts reveals speckles and lamina as hubs of functionally distinct retained introns.” Molecular cell vol. 82,5 (2022): 1035-1052.e9. doi:10.1016/j.molcel.2021.12.010 Fazal, Furqan M et al. “Atlas of Subcellular RNA Localization Revealed by APEX-Seq.” Cell vol. 178,2 (2019): 473-490.e26. doi:10.1016/j.cell.2019.05.027
APEXdb 是首个公开可用、经人工整理注释的数据集，专门面向依赖APEX的邻近生物素标记策略。本资源为研究者提供了一个集中化的研究枢纽，可用于探索蛋白质-RNA相互作用，并评估不同细胞环境下的空间转录组。 资源概览 PLANSdb 整合并注释了当前所有可获取的数据，这些数据围绕被鉴定为特定带有APEX标记的诱饵蛋白的相互作用因子或邻近分子的RNA。通过将分散的实验结果整合至统一的分析框架中，您可以： - 检索特定的蛋白质-RNA相互作用 - 评估已鉴定相互作用因子的特异性 - 区分非特异性的"背景"RNA与具有生物学意义的特异性相互作用 数据构成与元数据 为确保实验可重复性并便于跨研究比较，PLANSdb 中的每一条数据条目都附带了全面的实验元数据，具体包括： - 诱饵蛋白信息：所使用的标记类型及其特定的细胞定位 - 生物学背景：实验中使用的细胞系以及施加的特定应激条件 - 技术参数：测序所用的起始样本类型以及所采用的测序平台 整合与未来拓展 PLANSdb 并非静态资源，它整合了本项目内产生的新型数据，并设计为可持续拓展的平台。本团队将定期收录新产出的数据集，确保科研共同体能够获取最新的邻近标记研究相关信息。 目前，以下已发表文献的数据已被整合至该资源中： Padrón, Alejandro 等人：《APEX-Seq邻近RNA标记技术揭示翻译起始复合物与抑制性RNA颗粒的组织架构》，*Molecular Cell*，第75卷第4期（2019年）：875-887.e5，DOI: 10.1016/j.molcel.2019.07.030 Barutcu, A Rasim 等人：《核结构域相关转录本的系统性绘图揭示核斑点与核纤层为功能迥异的内含子滞留枢纽》，*Molecular Cell*，第82卷第5期（2022年）：1035-1052.e9，DOI: 10.1016/j.molcel.2021.12.010 Fazal, Furqan M 等人：《APEX-Seq揭示的亚细胞RNA定位图谱》，*Cell*，第178卷第2期（2019年）：473-490.e26，DOI: 10.1016/j.cell.2019.05.027
