Bridging dataset generation to enable integrated data analysis and interpretation across HuBMAP tissues

桥接数据集生成以实现跨 HuBMAP 组织的集成数据分析和解释

• 批准号: 10672692
• 负责人: LOUISE CHANG LAURENT
• 金额: $ 15万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-01 至 2023-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10672692
• 关键词: 3-Dimensional; ATAC-seq; Anatomy; Atlases; Benchmarking; Biological; Biological Assay; Biological Markers; Cell Count; Cell Line; Cell Nucleus; Cells; Chromium; Collection; Computer software; Data; Data Analyses; Data Set; Development; Ensure; Female; Freezing; Gene Expression; Gene Expression Profiling; Generations; Genomics; Goals; Heart; Human BioMolecular Atlas Program; Individual; Intestines; Kidney; Link; Lung; Manuscripts; Maps; Metadata; Neighborhoods; Organ; Preparation; Protocols documentation; Publications; Quality Control; Sampling; Site; Source; Standardization; Technology; Tissue Sample; Tissues; Work; XCL1 gene; cell type; cost; data integration; data portal; experimental study; male; meetings; multiple data types; novel; tissue mapping; transcriptome sequencing; working group

PROJECT SUMMARY The goal of this supplement is to generate bridging datasets across all HuBMAP tissues to allow the HuBMAP Consortium to aggregate and integrate data and metadata from each tissue with respect to anatomical references in a standardized manner to facilitate data integration, analysis and interpretation. We will perform the 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression assay on snap- frozen tissue samples for each organ across several Tissue Mapping Centers (TMC). This assay enables collection of RNAseq and ATACseq data that are linked at the single-cell/single-nucleus level. We will link the individual tissue 10x Multiome bridge datasets to each of the Anatomic, Structural, Cell Types and Biomarkers (ASCT+B) tables for each organ to build a framework to input into the HuBMAP HIVE’s Registration User Interface. We will ensure that these data (annotated with detailed biological and technical metadata) will be made available for broad use, including not only the building of 3D multiscale maps that are the primary goal of this Consortium, but also development of novel profiling technologies and computational approaches for analysis and integration of multiple data types across multiple tissue types. We will rapidly release these bridge datasets to the TMCs to be integrated with the organ-specific TMC spatial data to build spatially-resolved 3D tissue maps derived from this common bridging dataset. As the Co-Chair of the HuBMAP Integrated Data Analysis & Interpretation Working Group and through involvement with the Collaborative Projects and Publications Working Group planning the cross-tissue integrative data analysis manuscript, we identified this important gap in the HuBMAP Consortium datasets currently generated or planned to be generated at the HuBMAP 2022 Annual Meeting. Generating a bridging dataset across all HuBMAP tissues will create an anchor for all individual organ atlases and enable integrative analysis across consortium datasets to assess similarities and differences across tissues in cell count composition, cell types and states, neighborhoods and functional units.

项目摘要 本补充的目标是生成所有HuBMAP组织的桥接数据集，以允许HuBMAP 联合体，以聚合和整合来自每个组织的关于解剖结构的数据和元数据。 以标准化方式提供参考资料，以促进数据整合、分析和解释。我们将执行 速冻组织上的10 x基因组学铬单细胞多组ATAC +基因表达测定 在几个组织映射中心（TMC）的每个器官的样本。该测定能够收集RNAseq 以及在单细胞/单核水平上关联的ATACseq数据。我们将单个组织10倍连接 Multiome将数据集连接到每个解剖、结构、细胞类型和生物标志物（ASCT+B）表， 每个器官建立一个框架，输入到HuBMAP HIVE的注册用户界面。我们将确保 这些数据（附有详细的生物和技术元数据注释）将可供广泛使用， 不仅包括建立三维多尺度地图，这是该联盟的主要目标，而且 开发新的剖面技术和计算方法，用于分析和整合 跨多种组织类型的多种数据类型。我们将迅速向TMC发布这些桥接数据集， 与器官特异性TMC空间数据集成，以构建由此导出的空间分辨3D组织图 通用桥接数据集。作为HuBMAP综合数据分析和解释工作的联合主席 通过参与合作项目和出版物工作组， 跨组织综合数据分析手稿，我们确定了HuBMAP联盟的这一重要差距 目前生成或计划在HuBMAP 2022年会上生成的数据集。生成 跨所有HuBMAP组织的桥接数据集将为所有单个器官图谱创建锚，并使 跨联盟数据集的综合分析，以评估细胞计数中组织间的相似性和差异 组成、细胞类型和状态、邻域和功能单元。