Pregnant Female Reproductive Tissue Mapping Center Data Analysis Core
孕妇生殖组织图谱中心数据分析核心
基本信息
- 批准号:10531090
- 负责人:
- 金额:$ 22.18万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2022
- 资助国家:美国
- 起止时间:2022-08-01 至 2026-07-31
- 项目状态:未结题
- 来源:
- 关键词:3-DimensionalAdoptedAnatomyArchitectureAreaAtlasesBiological AssayCell CommunicationCell NucleusCellsCellular StructuresClinicalCollaborationsCollectionDataData AnalysesData SetDevelopmentEmerging TechnologiesEnsureExtracellular MatrixFAIR principlesFemaleFundingHuman BioMolecular Atlas ProgramHuman bodyImageImmunohistochemistryIndividualLinkMammalian OviductsMapsMediatingMetadataModalityMolecularMorphologyOrganPathologicPlacentaPlacentationPoliciesPregnancyProceduresQuality ControlRNASamplingSignal TransductionSoftware ToolsStructureSurveysTechniquesTissue ModelTissuesTouch sensationTranscriptUnited States National Institutes of HealthUterusVisualizationanalysis pipelinecell typecollaboratorycomputerized data processingdata analysis pipelinedata exchangedata formatdata integrationdata qualitydata standardsextracellularflexibilityimaging modalityin vivo imagingindexinginteroperabilitymetadata standardsmigrationmultiple data typesmultiscale dataorgan growthpregnantprogramsprotein expressionreproductivesecondary analysisspatiotemporaltissue mappingtooltranscriptomics
项目摘要
SUMMARY
The Data Analysis Core (DAC) of the HuBMAP Pregnant Female Reproductive Tissue Mapping Center (PFR
TMC) will perform analysis of each data type generated by the Organ Specific Project (OSP), as well as
integrative analysis of multiple data types aimed at building 3D multiscale tissue maps of the developing and
term pregnant placenta, and term uterine endomyometrium and fallopian tubes; exploration of extracellular RNA-
mediated signaling between the placental and maternal tissues; and tracking of cellular differentiation and
migration in the developing placenta across gestation. These integrative analyses will be facilitated by two
strategies: 1) collection of bridging datasets (datasets that link two data types, such as the 10x Multi-ome assay,
which collects snRNAseq/snATACseq indexed to the same nuclei, or GeoMX DSP WTA, in which the operator
uses tissue morphology and immunohistochemistry to select features for spatial transcriptomic profiling, thus
linking morphology and/or protein expression with transcript abundance); and 2) combining broad surveys of
small numbers of samples for many samples with deep spatial profiling of multiple serial sections from selected
exemplar tissue blocks to build detailed models of tissue architecture. The DAC will collaborate with the HuBMAP
Integration, Visualization & Engagement Collaboratory (HIVE) to build an atlas of 3D tissue maps in the context
of the whole human body. The DAC is responsible for data processing, annotation, metadata curation, analysis,
and map construction within the PFR TMC. The DAC interacts closely with the OSP and coordinates interactions
with the other HuBMAP TMCs, HIVE and NIH Program staff. The DAC ensures that data, metadata, software
and tools will be open, findable, accessible, interoperable, reusable (FAIR) and maintains flexibility to adapt
processing and analysis capabilities to emerging technologies within the HuBMAP Consortium. The DAC has
assembled a PFR TMC Data Release Team comprised of experts in each of the included data modalities that
interfaces directly with the HIVE to ensure data quality control, metadata standards and facilitate data transfer.
The DAC collaborates closely with the HIVE to optimize secondary analysis pipelines and to implement the
Registration User Interface to register tissue sections to reference organs and a Common Coordinate Framework
to fully integrate spatial and molecular data across individuals. Since the establishment of the PFR TMC 15
months ago, the DAC has been involved in development of Consortium-wide metadata standards, data quality
metrics, analysis techniques and data structures, particular in the areas touching upon the specific data and
tissue types utilized by the PFR TMC.
摘要
HuBMAP孕期女性生殖组织测绘中心数据分析核心(DAC)
TMC)将对器官特定项目(OSP)生成的每种数据类型进行分析,以及
多种数据类型的综合分析,旨在建立正在发育的和
足月妊娠胎盘、足月子宫肌层和输卵管;细胞外RNA的探索
胎盘和母体组织之间的中介信号;细胞分化和细胞分化的跟踪
妊娠期间发育中的胎盘的迁移。这些综合分析将由两个
策略:1)桥接数据集(链接两种数据类型的数据集,例如10倍多基因组分析,
它收集索引到相同核或GeoMX DSP WTA的SnRNAseq/SnATACseq,其中操作员
使用组织形态和免疫组织化学来选择空间转录图谱的特征,因此
将形态和/或蛋白质表达与转录本丰度联系起来);以及2)结合对
从精选的多个序列剖面进行深空间剖面图的小样本多样本
样本组织块,以建立详细的组织结构模型。DAC将与HuBMAP合作
集成、可视化和参与性合作实验室(HIVE),以构建上下文中的3D组织图图集
整个人类的身体。DAC负责数据处理、注释、元数据整理、分析、
以及PFR TMC内的地图构建。DAC与OSP密切互动并协调互动
与其他HuBMAP TMC、HIVE和NIH计划工作人员一起。DAC确保数据、元数据、软件
工具将是开放的、可查找的、可访问的、可互操作的、可重复使用的(公平的),并保持适应的灵活性
对HuBMAP联盟内的新兴技术的处理和分析能力。DAC有
组建了一个PFR TMC数据发布团队,该团队由以下每种数据模式的专家组成
直接与蜂巢接口,以确保数据质量控制、元数据标准和促进数据传输。
DAC与HIVE密切合作,以优化二次分析管道并实施
用于将组织切片与参考器官配准的配准用户界面和公共坐标框架
完全集成各个个体的空间和分子数据。自PFR TMC 15成立以来
几个月前,发改委参与了联盟范围内元数据标准、数据质量的开发
指标、分析技术和数据结构,特别是在涉及特定数据和
PFR TMC使用的组织类型。
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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Kathleen Marie Fisch其他文献
Kathleen Marie Fisch的其他文献
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{{ truncateString('Kathleen Marie Fisch', 18)}}的其他基金
Genomic Dissection of Placental Lesions in Preeclampsia
先兆子痫胎盘病变的基因组解剖
- 批准号:
10742701 - 财政年份:2023
- 资助金额:
$ 22.18万 - 项目类别:
Pregnant Female Reproductive Tissue Mapping Center Data Analysis Core
孕妇生殖组织图谱中心数据分析核心
- 批准号:
10670433 - 财政年份:2022
- 资助金额:
$ 22.18万 - 项目类别:
Pregnant Female Reproductive Tissue Mapping Center Data Analysis Core
孕妇生殖组织图谱中心数据分析核心
- 批准号:
10701367 - 财政年份:2022
- 资助金额:
$ 22.18万 - 项目类别:
Female Reproductive Tissue Mapping Center Data Analysis Core
女性生殖组织图谱中心数据分析核心
- 批准号:
10119156 - 财政年份:2020
- 资助金额:
$ 22.18万 - 项目类别:
Female Reproductive Tissue Mapping Center Data Analysis Core
女性生殖组织图谱中心数据分析核心
- 批准号:
10268241 - 财政年份:2020
- 资助金额:
$ 22.18万 - 项目类别:
Omics Data Generation Center (ODGC) for the Acute to Chronic Pain Signatures (A2CPS) Program
急性至慢性疼痛特征 (A2CPS) 计划的组学数据生成中心 (ODGC)
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10000873 - 财政年份:2019
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$ 22.18万 - 项目类别:
Omics Data Generation Center (ODGC) for the Acute to Chronic Pain Signatures (A2CPS) Program
急性至慢性疼痛特征 (A2CPS) 计划的组学数据生成中心 (ODGC)
- 批准号:
10224832 - 财政年份:2019
- 资助金额:
$ 22.18万 - 项目类别:
Omics Data Generation Center (ODGC) for the Acute to Chronic Pain Signatures (A2CPS) Program
急性至慢性疼痛特征 (A2CPS) 计划的组学数据生成中心 (ODGC)
- 批准号:
10680641 - 财政年份:2019
- 资助金额:
$ 22.18万 - 项目类别:
Omics Data Generation Center (ODGC) for the Acute to Chronic Pain Signatures (A2CPS) Program
急性至慢性疼痛特征 (A2CPS) 计划的组学数据生成中心 (ODGC)
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10415817 - 财政年份:2019
- 资助金额:
$ 22.18万 - 项目类别:
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