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: 10552968
• 负责人: Sheng Li
• 金额: $ 82.87万
• 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/10552968
• 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; Small Nuclear RNA; Standardization; Testing; The Jackson Laboratory; Tissues; aged; analysis pipeline; base; cell type; cohort; computerized data processing; data management; data sharing networks; deep learning; design; imaging Segmentation; mass spectrometric imaging; novel marker; open source; process optimization; prospective; response; senescence; 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.

项目摘要/摘要数据分析核心 JAX-SEN小鼠组织映射中心（TMC）的数据分析核心（DAC）的目的是 构建小鼠细胞衰老的生物标志物数据集和分子图，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的of将产生高分辨率的高含量分子数据，以表征细胞衰老 小鼠肾脏，脂肪组织，胰腺，胎盘，心脏和下丘脑，年龄，近交和遗传学 多样的小鼠队列。从这些数据中，DAC将建立最先进的工作流以进行数据注释， 策划和分析转录组，成像和成像质谱（IMS）数据以构建细胞 衰老图。 DAC将与Jax和UConn的人类Sennet TMC的DAC紧密合作 健康（Kapp-sen TMC），其他人和鼠标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的最新进展，以定义衰老细胞的强大生物标志物 并绘制其组织环境。为了实现其目标，JAX-SEN DAC将实施严格且可重复的 数据注释，策展，处理和传播（AIM 1）。 DAC将接收并集中 来自JAX-SEN BAC的测序，成像和IMS数据。它将自动化并硬化QC程序以筛选 对于注释和策展误差，与BAC合作，批处理效应和低质量样本。这 DAC将根据共同社区标准，JAX-SEN和 参考数据集，然后容器以与CODCC共享。从这些数据中，JAX-SEN DAC将 构建细胞衰老的生物标志物数据集和分子图（AIM 2）。 DAC将部署分析 用于测序，图像和IMS数据的管道，具有已知和前瞻性衰老标记，以识别和 在功能上注释衰老细胞的新型生物标志物并绘制其组织环境，计算多样性 在衰老细胞群体中，并量化衰老细胞与邻近之间的细胞间相互作用 细胞。 DAC将汇总并整合这些数据和元数据以构建高质量的细胞图 衰老。最后，JAX-SEN DAC将使用严格且可重复的开放 - 来源处理管道（AIM 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，以及网络数据共享策略，以确切可重复性。我们将与Kapp-Sen合作， 其他CODCC项目和TMC识别协同作用，例如，在同一的人类和鼠标生物标志物中对齐 组织。