Center for High Throughput Sequencing, Core Facility for Protein Research, Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
Nucleic Acids Res. 2020 Jan 8;48(D1):D233-D237. doi: 10.1093/nar/gkz934.
Spatially resolved transcriptomic techniques allow the characterization of spatial organization of cells in tissues, which revolutionize the studies of tissue function and disease pathology. New strategies for detecting spatial gene expression patterns are emerging, and spatially resolved transcriptomic data are accumulating rapidly. However, it is not convenient for biologists to exploit these data due to the diversity of strategies and complexity in data analysis. Here, we present SpatialDB, the first manually curated database for spatially resolved transcriptomic techniques and datasets. The current version of SpatialDB contains 24 datasets (305 sub-datasets) from 5 species generated by 8 spatially resolved transcriptomic techniques. SpatialDB provides a user-friendly web interface for visualization and comparison of spatially resolved transcriptomic data. To further explore these data, SpatialDB also provides spatially variable genes and their functional enrichment annotation. SpatialDB offers a repository for research community to investigate the spatial cellular structure of tissues, and may bring new insights into understanding the cellular microenvironment in disease. SpatialDB is freely available at https://www.spatialomics.org/SpatialDB.
空间分辨转录组学技术允许对组织中细胞的空间组织进行特征描述，这彻底改变了组织功能和疾病病理学的研究。新的检测空间基因表达模式的策略正在涌现，空间分辨转录组学数据正在迅速积累。然而，由于策略的多样性和数据分析的复杂性，生物学家利用这些数据并不方便。在这里，我们展示了 SpatialDB，这是第一个用于空间分辨转录组学技术和数据集的手动编目数据库。目前的版本包含 5 个物种的 24 个数据集（305 个子数据集），由 8 种空间分辨转录组学技术生成。SpatialDB 提供了一个用户友好的 Web 界面，用于可视化和比较空间分辨转录组学数据。为了进一步探索这些数据，SpatialDB 还提供了空间变化基因及其功能富集注释。SpatialDB 为研究社区提供了一个研究组织中空间细胞结构的存储库，并可能为理解疾病中的细胞微环境带来新的见解。SpatialDB 可在 https://www.spatialomics.org/SpatialDB 免费获取。
