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.

项目概要 本补充的目标是生成跨所有 HuBMAP 组织的桥接数据集，以允许 HuBMAP 联盟聚合和整合来自每个组织的解剖学数据和元数据 我们将以标准化的方式进行参考，以促进数据整合、分析和解释。 对速冻组织进行 10x Genomics Chromium 单细胞多组 ATAC + 基因表达测定 跨多个组织作图中心 (TMC) 的每个器官的样本 该测定可以收集 RNAseq。 以及在单细胞/单核水平上链接的 ATACseq 数据，我们将链接各个组织 10x。 将多组数据集桥接至每个解剖、结构、细胞类型和生物标志物 (ASCT+B) 表 我们将确保每个机构建立一个框架以输入 HuBMAP HIVE 的注册用户界面。 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， 不仅包括构建 3D 多比例地图（该联盟的主要目标），还包括 开发新的分析技术和计算方法来分析和集成 我们将快速将这些桥梁数据集发布给 TMC。 与器官特异性 TMC 空间数据集成，构建由此衍生的空间分辨 3D 组织图 作为 HuBMAP 综合数据分析和解释工作的联合主席。 小组并通过参与合作项目和出版物工作组规划 跨组织综合数据分析手稿，我们发现了 HuBMAP 联盟中的这一重要差距 当前生成或计划在 HuBMAP 2022 年会上生成的数据集。 跨所有 HuBMAP 组织的桥接数据集将为所有单个器官图谱创建一个锚点，并启用 跨联盟数据集的综合分析，以评估不同组织细胞计数的相似性和差异 组成、细胞类型和状态、邻域和功能单元。