A visualization interface for BRAIN single cell data, integrating transcriptomics, epigenomics and spatial assays

BRAIN 单细胞数据的可视化界面，集成转录组学、表观基因组学和空间分析

• 批准号: 10643313
• 负责人: Maximilian Haeussler
• 金额: $ 86.63万
• 依托单位: UNIVERSITY OF CALIFORNIA SANTA CRUZ
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-04-01 至 2026-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10643313
• 关键词: Acceleration; Address; Adopted; Algorithmic Analysis; Algorithms; Archives; Atlases; BRAIN initiative; Biological Assay; Biological Sciences; Brain; Cells; Cellular Assay; Censuses; Chromosomes; Collection; Computer Analysis; Computer software; Custom; Data; Data Analyses; Data Display; Data Files; Data Set; Databases; Dimensions; Environment; Funding; Future; Gene Expression; Genes; Genomics; Hour; Human; Image; Internet; Knowledge; Location; Maps; Metadata; Methylation; Microscopy; Modality; Molecular; Online Systems; Ontology; Pattern; Physiology; Process; Provider; Publications; Reaction Time; Research Personnel; Retrieval; Risk; Running; Security; Side; Slice; Specific qualifier value; Standardization; Structure; Technology; Testing; Time; United States National Institutes of Health; Universities; Visualization; Visualization software; Work; Writing; XCL1 gene; brain cell; cell type; cloud storage; computerized tools; data access; data archive; data centers; data management; data portal; data reuse; data sharing; data structure; data visualization; design; differential expression; distributed archives; epigenomics; field study; file format; flexibility; genome browser; improved; interest; open data; sex; success; tool; transcriptomics; user-friendly; web site

PROJECT SUMMARY / ABSTRACT The BRAIN Initiative’s -omics data archive NeMO contains all the BICCN single cell single cell data, more than one million files at the time of writing. However, no interactive visualization interface to inspect these results is available and many researchers are not proficient enough with computational tools (download data, convert, load, plot) to take advantage of the data in NeMO. This makes testing hypotheses by non-computational researchers a lot harder than necessary but the input from these domain experts and their knowledge about molecular processes and cell specification is crucial for the interpretation of the data. Here, I propose to repeat for the single cell field what has made genome browsers a pillar of data sharing: a standard file format and a visualization tool for it. A new format is a requirement, because in the era of cloud technology and distributed archives, data is usually not stored locally anymore. Sub-second reaction times from remote storage are necessary for visualization and possible but existing single cell file formats were not designed for this access pattern. In addition, for NeMO, being able to keep all results of a single cell assay in one defined structure makes data management and access easier. We will define such a format, it will integrate all the main analysis results and will convert all existing processed data in NeMO (not the raw read data) to the new format. We will then make the data available for interactive exploration directly on the NeMO website via our UCSC Cell Browser, which is already running on different University websites. It is actively used already by thousands of researchers every month to visualize hundreds of single datasets that we collected at UCSC and has been used for hundreds of scientific publications. We will extend our tool to provide direct support for the most recent assay and analysis types, mainly ATAC, methylation and spatial transcriptomics imaging data and integrate the UCSC Genome Browser for chromosome-level views and summaries. An improved split-screen mode will allow visualizing both spatial and transcriptomic data at the same time. In addition, the Cell Browser will allow users to run the most fundamental and well-known analysis algorithms on any subset of cells, with a focus on fast response time so that researchers do not have to download the whole dataset to get differential genes, dimensionality reduction or specific sub-clustering results of a few selected cell clusters of interest. Integrating these software features and the NeMO data into a single user-friendly environment will make sure that the BICCN -omics data can be accessed as easily as possible, which will help accelerate the path to discovery from the wealth of BRAIN single cell datasets being produced right now and in the future.

项目概要/摘要 BRAIN Initiative 的 -omics 数据档案 NeMO 包含所有 BICN 单细胞单细胞数据，更多 在撰写本文时超过一百万个文件。然而，没有交互式可视化界面来检查这些 结果是可用的，但许多研究人员对计算工具不够熟练（下载数据、 转换、加载、绘图）以利用 NeMO 中的数据。这使得通过以下方式检验假设 非计算研究人员的难度比必要的要大得多，但这些领域专家及其他们的输入 有关分子过程和细胞规格的知识对于数据的解释至关重要。 在这里，我建议在单细胞领域重复一下基因组浏览器成为数据共享支柱的原因： 标准文件格式及其可视化工具。需要一种新的格式，因为在云时代 技术和分布式档案，数据通常不再存储在本地。亚秒级反应时间 来自远程存储的数据对于可视化是必要的并且是可能的，但现有的单单元文件格式不是 专为这种访问模式而设计。此外，对于 NeMO 来说，能够将单细胞测定的所有结果保存在 一种定义的结构使数据管理和访问变得更加容易。我们将定义这样一个格式，它将 整合所有主要分析结果，并将转换 NeMO 中所有现有的处理数据（不是原始读取的数据） 数据）转换为新格式。 然后，我们将通过 UCSC 直接在 NeMO 网站上提供数据，用于交互式探索 Cell Browser，已经在不同的大学网站上运行。它已被数千人积极使用 的研究人员每个月都会对我们在 UCSC 收集的数百个单一数据集进行可视化 用于数百种科学出版物。我们将扩展我们的工具，为最新的 检测和分析类型，主要是ATAC、甲基化和空间转录组学成像数据并整合 UCSC 基因组浏览器用于染色体级别的视图和摘要。改进的分屏模式将 允许同时可视化空间和转录组数据。此外，Cell Browser 将允许 用户可以对任何细胞子集运行最基本和众所周知的分析算法，重点是 响应时间快，研究人员无需下载整个数据集即可获取差异基因， 一些选定的感兴趣的细胞簇的降维或特定子聚类结果。 将这些软件功能和 NeMO 数据集成到一个用户友好的环境中将使 确保 BICCN 组学数据可以尽可能轻松地访问，这将有助于加速 从现在和未来产生的大量 BRAIN 单细胞数据集中发现。