Alzheimer’s Disease (AD) pathology has been increasingly explored through single-cell and single-nucleus RNA-sequencing (scRNA-seq & snRNA-seq) and spatial transcriptomics (ST). However, the surge in data dema
The spatial transcriptomics data of the MERFISH human brain dataset are available at Dryad (https://doi.org/10.5061/dryad.x3ffbg7mw). The section of H22.26.401.MTG.4000 was used in this study. Experimental RNA subcellular localization data are available in the RNALocate v.2.0 database (...
Alzheimer's Disease (AD) pathology has been increasingly explored through single-cell and single-nucleus RNA-sequencing (scRNA-seq & snRNA-seq) and spatial transcriptomics (ST). However, the surge in data demands a comprehensive, user-friendly repository. Addressing this, we introduce a single-...
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...
Spatial Omics DataBase SpaCET: Spatial Cellular Estimator for Tumors sST: Sequencing based ST ST: Spatial transcriptomics STRS: Spatial total RNA sequencing TAM: Tumor-associated macrophages TIB: Tumor immune barrier TIF: Tumor invasion front TIME: Tumor immune microenvironment TLS: Terti...
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...
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....
While spatial transcriptomics offer valuable insights into gene expression patterns within the spatial context of tissue, many technologies do not have a single-cell resolution. Here, we present SMART, a marker gene-assisted deconvolution method that sim
Workflow and functionality of the Bento toolkit.ASingle-molecule resolved spatial transcriptomics data from commercial or custom platforms are ingested into Bento where it is converted to the AnnData format (B), where it can be manipulated with Bento as well as a wide ecosystem of single-cell omi...
STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization 2024, Nucleic Acids Research Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value 2021, Frontiers in Plant Science Single-Cell RNA Sequencing for Plant Research: Insights...