Here, we describe a database, SPathDB (http://bio-bigdata.hrbmu.edu.cn/SPathDB/), which aims to dissect the pathway-mediated multidimensional spatial heterogeneity in the context of functional activity. We manually curated spatial transcriptomics datasets and biological pathways from public data ...
In conclusion, the integration of spatial transcriptomics with scRNA data in this investigation enabled the identification of a comprehensive spatial gene expression profile and specific functions in an individual kidney region and provided an understanding of the variations in the spatiotemporal gene landsc...
Data availability The database of spatial transcriptomics literature can be accessed at https://docs.google.com/spreadsheets/d/1sJDb9B7AtYmfKv4-m8XR7uc3XXw_k4kGSout8cqZ8bY/edit#gid=1363594152. The version used as of writing is in the metadata.xlsx file in the frozen DOI version of the ...
Data availability The database of spatial transcriptomics literature can be accessed at https://docs.google.com/spreadsheets/d/1sJDb9B7AtYmfKv4-m8XR7uc3XXw_k4kGSout8cqZ8bY/edit#gid=1363594152. The version used as of writing is in the metadata.xlsx file in the frozen DOI version of the ...
Spatial transcriptomics (ST) has filled this gap and has been widely used in respiratory studies. This review focuses on the latest iterative technology of ST in recent years, summarizing how ST can be applied to the physiological and pathological processes of the respiratory system, with emphasis...
SOAR: a spatial transcriptomics analysis resource to model spatial variability and cell type interactions. Preprint at bioRxiv https://doi.org/10.1101/2022.04.17.488596 (2022). Fan, Z., Chen, R. & Chen, X. SpatialDB: a database for spatially resolved transcriptomes. Nucleic Acids Res. https:...
Data and images of in situ sequencing This paper https://repo-prod.prod.sagebase.org/repo/v1/doi/locate?id=syn22153884&type=ENTITY Resource website including sequence data, images, analyses, and resources related to the Spatial Transcriptomics and in situ sequencing of mouse and human samples....
Molecular signature data base ROI: Region of interest scRNAseq: Single cell RNA sequencing scSpatial Explorer: Single-cell spatial explorer ST: Spatial transcriptomics t-SNE: t-Distributed stochastic neighbour embedding UMAP: Uniform manifold approximation and projection ...
systems being studied; 2. select the best-suited spatial transcriptomics technique; 3. maximize output from spatial transcriptomic studies using complementary data such as single-cell transcriptome reference data and auxiliary stains; and 4. analyse these data with specialized algorithms for spatial -...
Pairpot: a database with real-time lasso-based analysis tailored for paired single-cell and spatial transcriptomics Paired single-cell and spatially resolved transcriptomics (SRT) data supplement each other, providing in-depth insights into biological processes and disea... R Zhihan,F Lin,Z Zhang...