Data Analysis Core

数据分析核心

• 批准号: 10531082
• 负责人: SYLVIA KATINA PLEVRITIS
• 金额: $ 43.55万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-23 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10531082
• 关键词: 3-Dimensional; ATAC-seq; Address; Antibodies; Architecture; Benchmarking; Blood Vessels; Cell Nucleus; Cells; Chromium; Colon; Communities; Data; Data Analyses; Enterocytes; Fluorescent in Situ Hybridization; Funding; Genes; Genetic Transcription; Heterogeneity; Human; Human BioMolecular Atlas Program; Image; Immune; Immunoassay; Infrastructure; Intestines; Investigation; Maps; Metadata; Methods; Molecular; Muscle; Neighborhoods; Nuclear RNA; Ontology; Organ; Phase; Population; Process; Production; Proteins; Protocols documentation; Quality Control; RNA; Reproducibility; Resolution; Resources; Site; Small Intestines; Software Engineering; Software Framework; Standardization; Statistical Methods; Structure; System; Thick; Tissues; analysis pipeline; cell type; cloud based; computerized data processing; data analysis pipeline; data modeling; data quality; data standards; epigenomics; experience; human data; interoperability; multimodal data; multimodality; multiplex assay; next generation; novel; open source; platform-independent; programs; public repository; relating to nervous system; software development; tissue mapping; tool; transcriptome; transcriptome sequencing; transcriptomics; working group

ABSTRACT: Data Analysis Core In our investigation of the cellular architecture of bowel tissue, we will continue to generate multimodal single-cell resolution data. Using the Chromium Multiome platform, we generate simultaneous single-nuclei RNA+ATAC-seq to profile the gene transcription and regulatory programs of cells. We have defined previously-described cell populations as well as novel cell types and sub-types. Our spatial data will be mapped through two highly multiplexed assays: the CODEX immunoassay and the Molecular Cartography FISH assay. Because CODEX throughput can be scaled, we will use it to map serial sections that will be reconstructed to make three-dimensional maps. Molecular Cartography will provide a complementary transcriptome map to enable more accurate integration of the single-nuclei data to the CODEX maps. We have existing standardized pipelines to process each of these data types. We also have tools to integrate these multi-modal data types. We will continue to refine these integrative methods as we investigate our proposed organ of focus along with other organs in coordination with HuBMAP. All of our data will be submitted to the HIVE and public repositories for broad access to the community.

摘要：数据分析核心 在我们对肠组织细胞结构的研究中，我们将继续产生 多模态单细胞分辨率数据。使用 Chromium Multiome 平台，我们生成 同时单核 RNA+ATAC-seq 分析基因转录和调控 细胞程序。我们已经定义了先前描述的细胞群以及新细胞 类型和子类型。我们的空间数据将通过两种高度多重分析来绘制： CODEX 免疫测定和分子制图 FISH 测定。因为法典 吞吐量可以缩放，我们将使用它来映射将被重建的串行部分，以使得 三维地图。分子制图将提供互补的转录组 图，以便更准确地将单核数据整合到 CODEX 图上。我们 拥有现有的标准化管道来处理每种数据类型。我们还有工具 集成这些多模式数据类型。我们将继续完善这些综合方法 我们与其他机构一起调查我们提议的重点机构 HuBMAP。我们所有的数据都将提交到 HIVE 和公共存储库以供广泛访问 到社区。