The Jackson Laboratory Senescence Tissue Mapping Center (JAX-Sen TMC) - Data Analysis Core

杰克逊实验室衰老组织绘图中心 (JAX-Sen TMC) - 数据分析核心

• 批准号: 10683393
• 负责人: Sheng Li
• 金额: $ 104.73万
• 依托单位: JACKSON LABORATORY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-08-15 至 2026-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10683393
• 关键词: Adipose tissue; Age; Aging; Antibodies; Atlases; Benchmarking; Biologic Characteristic; Biological; Biological Markers; Cell Aging; Cell Communication; Cells; Classification; Collaborations; Common Data Element; Communities; Computational Biology; Computer Vision Systems; Data; Data Analyses; Data Analytics; Data Coordinating Center; Data Set; Development; Generations; Genetic; Goals; Health; Heart; Human; Hypothalamic structure; Image; Inbreeding; Individual; Kidney; Linear Models; Maps; Mass Spectrum Analysis; Metadata; Modality; Molecular; Mouse Strains; Mus; Nuclear RNA; Pancreas; Pathway Analysis; Placenta; Policies; Population; Preparation; Procedures; Process; Proteomics; RLK5-associated protein phosphatase; Reproducibility; Resolution; Sampling; Standardization; Testing; The Jackson Laboratory; Tissues; Visualization; aged; analysis pipeline; cell type; cohort; computerized data processing; data integration; data management; data sharing networks; deep learning; design; imaging Segmentation; mass spectrometric imaging; novel marker; open source; process optimization; prospective; response; senescence; single nucleus RNA-sequencing; single-cell RNA sequencing; synergism; tissue mapping; tool; transcriptome; transcriptome sequencing; transcriptomics

PROJECT SUMMARY/ABSTRACT DATA ANALYSIS CORE The objective of the Data Analysis Core (DAC) of the JAX-Sen mouse Tissue Mapping Center (TMC) is to construct biomarker datasets and molecular maps of cellular senescence in mice and deliver these data to the SenNet Consortium Organization and Data Coordinating Center (CODCC). The Biological Analysis Core (BAC) of JAX-Sen will generate high-resolution, high-content molecular data to characterize cellular senescence in mouse kidney, adipose tissue, pancreas, placenta, heart and hypothalamus in aged, inbred and genetically diverse mouse cohorts. From these data, the DAC will establish state-of-the-art workflows for data annotation, curation, and analysis of transcriptomic, imaging, and imaging mass spectrometry (IMS) data to build cellular senescence maps. The DAC will collaborate closely with the DAC of the human SenNet TMC at JAX and UConn Health (KAPP-Sen TMC), other human and mouse TMCs and the CODCC to develop and implement Network- wide standards for processing, analyzing and visualizing SenNet data. The JAX-Sen DAC will leverage significant recent advances in deep learning and computer vision to define robust biomarkers of senescent cells and map their tissue context. To achieve its goals, the JAX-Sen DAC will implement rigorous and reproducible data annotation, curation, processing, and dissemination (Aim 1). The DAC will receive and centralize sequencing, imaging, and IMS data from the JAX-Sen BAC. It will automate and harden QC procedures to screen for annotation and curation errors, batch effects, and low-quality samples in collaboration with the BAC. The DAC will implement the pipelines based on common community standards, benchmark on JAX-Sen and reference datasets, and then containerize for sharing with the CODCC. From these data, the JAX-Sen DAC will construct biomarker datasets and molecular maps of cellular senescence (Aim 2). The DAC will deploy analysis pipelines for sequencing, image and IMS data with known and prospective senescence markers to identify and functionally annotate novel biomarkers of senescent cells and map their tissue context, compute the diversity within senescent cell populations, and quantify cell-to-cell interactions between senescent cells and neighboring cells. The DAC will aggregate and integrate these data and metadata to build high-quality maps of cellular senescence. Finally, the JAX-Sen DAC will disseminate JAX-Sen data with rigorous and reproducible open- source processing pipelines (Aim 3). The DAC will harmonize, standardize, and disseminate data processing and analytic pipelines with the CODCC, adhering to common community standards, standard operating procedures, and the network data sharing policy to exact reproducibility. We will collaborate with KAPP-Sen and other CODCC projects and TMCs to identify synergy, e.g., align human and mouse biomarkers on the same tissues.

项目概要/抽象数据分析核心 JAX-Sen 小鼠组织作图中心 (TMC) 的数据分析核心 (DAC) 的目标是 构建小鼠细胞衰老的生物标志物数据集和分子图谱，并将这些数据传递给 SenNet 联盟组织和数据协调中心 (CODCC)。生物分析核心 (BAC) JAX-Sen 将生成高分辨率、高含量的分子数据来表征细胞衰老 老年、近交和遗传小鼠肾脏、脂肪组织、胰腺、胎盘、心脏和下丘脑 不同的小鼠群体。根据这些数据，DAC 将建立最先进的数据注释工作流程， 整理和分析转录组、成像和成像质谱 (IMS) 数据以构建细胞 衰老图。 DAC 将与 JAX 和康涅狄格大学人类 SenNet TMC 的 DAC 密切合作 健康（KAPP-Sen TMC）、其他人类和小鼠 TMC 以及 CODCC 开发和实施网络- 用于处理、分析和可视化 SenNet 数据的广泛标准。 JAX-Sen DAC 将利用 深度学习和计算机视觉领域的最新重大进展定义了衰老细胞的稳健生物标志物 并绘制它们的组织背景图。为了实现其目标，JAX-Sen DAC 将实施严格且可重复的 数据注释、管理、处理和传播（目标 1）。 DAC 将接收并集中 来自 JAX-Sen BAC 的测序、成像和 IMS 数据。它将自动化和强化 QC 程序以进行筛选 与 BAC 合作解决注释和管理错误、批次效应和低质量样本问题。这 DAC 将根据通用社区标准、JAX-Sen 基准和 参考数据集，然后容器化以便与 COCDCC 共享。根据这些数据，JAX-Sen DAC 将 构建细胞衰老的生物标志物数据集和分子图（目标 2）。 DAC 将部署分析 用于测序、图像和 IMS 数据的管道，具有已知和预期的衰老标记，以识别和 对衰老细胞的新生物标志物进行功能注释并绘制其组织背景，计算多样性 衰老细胞群内，并量化衰老细胞与邻近细胞之间的细胞间相互作用 细胞。 DAC 将聚合并集成这些数据和元数据，以构建高质量的蜂窝地图 衰老。最后，JAX-Sen DAC 将以严格且可重复的开放方式传播 JAX-Sen 数据。 源处理管道（目标 3）。 DAC 将协调、标准化和传播数据处理 和 CODCC 的分析管道，遵守共同的社区标准、标准操作 程序和网络数据共享政策以实现精确的再现性。我们将与 KAPP-Sen 合作 其他 CODCC 项目和 TMC 以确定协同作用，例如，将人类和小鼠生物标志物对齐到相同的位置 组织。