A database for spatially resolved transcriptomes
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A database for spatially resolved transcriptomes
metasource: Fairsharing.org
version: FAIRsharing.org: SpatialDB; A database for spatially resolved transcriptomes; DOI: https://doi.org/10.25504/FAIRsharing.0Hsbor; Last edited: Dec. 19, 2019, 11:06 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
SpatialDB
metasource: Fairsharing.org
version: FAIRsharing.org: SpatialDB; A database for spatially resolved transcriptomes; DOI: https://doi.org/10.25504/FAIRsharing.0Hsbor; Last edited: Dec. 19, 2019, 11:06 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:27.619371
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:27.619371
SpatialDB: a database for spatially resolved transcriptomes
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Names
More detailed information about this field from each metasource.
A database for spatially resolved transcriptomes
metasource: Fairsharing.orgversion: FAIRsharing.org: SpatialDB; A database for spatially resolved transcriptomes; DOI: https://doi.org/10.25504/FAIRsharing.0Hsbor; Last edited: Dec. 19, 2019, 11:06 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
SpatialDB
metasource: Fairsharing.orgversion: FAIRsharing.org: SpatialDB; A database for spatially resolved transcriptomes; DOI: https://doi.org/10.25504/FAIRsharing.0Hsbor; Last edited: Dec. 19, 2019, 11:06 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:27.619371
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:27.619371
SpatialDB: a database for spatially resolved transcriptomes
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Other names: SpatialDB, SpatialDB: a database for spatially resolved transcriptomes
Names
More detailed information about this field from each metasource.
A database for spatially resolved transcriptomes
metasource: Fairsharing.orgversion: FAIRsharing.org: SpatialDB; A database for spatially resolved transcriptomes; DOI: https://doi.org/10.25504/FAIRsharing.0Hsbor; Last edited: Dec. 19, 2019, 11:06 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
SpatialDB
metasource: Fairsharing.orgversion: FAIRsharing.org: SpatialDB; A database for spatially resolved transcriptomes; DOI: https://doi.org/10.25504/FAIRsharing.0Hsbor; Last edited: Dec. 19, 2019, 11:06 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:27.619371
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:27.619371
SpatialDB: a database for spatially resolved transcriptomes
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Spatially resolved transcriptomics providing gene expression profiles with positional information is key to tissue function and fundamental to disease pathology. SpatialDB is the first public database that specifically curates spatially resolved transcriptomic data from published papers, aiming to provide a comprehensive and accurate resource of spatial gene expression profiles in tissues. Currently, SpatialDB contains detailed information of 24 datasets generated by 8 spatially resolved transcriptomic techniques. SpatialDB allows users to browse the spatial gene expression profile of all the 8 techniques online and compare the spatial gene expression profile of any two datasets generated by the same or different techniques side by side. It provides spatially variable (SV) genes identified by SpatialDE and trendsceek, as well as functional enrichment annotation of SV genes.
Description
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Spatially resolved transcriptomics providing gene expression profiles with positional information is key to tissue function and fundamental to disease pathology. SpatialDB is the first public database that specifically curates spatially resolved transcriptomic data from published papers, aiming to provide a comprehensive and accurate resource of spatial gene expression profiles in tissues. Currently, SpatialDB contains detailed information of 24 datasets generated by 8 spatially resolved transcriptomic techniques. SpatialDB allows users to browse the spatial gene expression profile of all the 8 techniques online and compare the spatial gene expression profile of any two datasets generated by the same or different techniques side by side. It provides spatially variable (SV) genes identified by SpatialDE and trendsceek, as well as functional enrichment annotation of SV genes.
metasource: Fairsharing.orgversion: FAIRsharing.org: SpatialDB; A database for spatially resolved transcriptomes; DOI: https://doi.org/10.25504/FAIRsharing.0Hsbor; Last edited: Dec. 19, 2019, 11:06 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
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.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
a database for spatially resolved transcriptomes. Welcome to SpatialDB! click thumbnails to quickly browse the spatial gene expression profiles. Spatially resolved transcriptomics providing gene expression profiles with positional information is key to tissue function and fundamental to disease pathology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:27.619371
Webpage:
https://www.spatialomics.org/SpatialDB/Webpage
More detailed information about this field from each metasource.
https://www.spatialomics.org/SpatialDB/
metasource: Fairsharing.orgversion: FAIRsharing.org: SpatialDB; A database for spatially resolved transcriptomes; DOI: https://doi.org/10.25504/FAIRsharing.0Hsbor; Last edited: Dec. 19, 2019, 11:06 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
https://www.spatialomics.org/SpatialDB
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:27.619371
Publications:
Publications
More detailed information about this field from each metasource.
SpatialDB: a database for spatially resolved transcriptomes
PMID: 31713629
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:27.619371
http://dx.doi.org/10.1093/nar/gkz934
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
SpatialDB: a database for spatially resolved transcriptomes
PMID: 31713629
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:27.619371
http://dx.doi.org/10.1093/nar/gkz934
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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SpatialDB: a database for spatially resolved transcriptomes
PubMed citations: 17.
17 articles citing: SpatialDB: a database for spatially resolved transcriptomes
JMJD8 Is an M2 Macrophage Biomarker, and It Associates With DNA Damage Repair to Facilitate Stemness Maintenance, Chemoresistance, and Immunosuppression in Pan-Cancer. PMID:35898493
Comprehensive Analysis of the Expression and Prognostic Value of LMAN2 in HER2+ Breast Cancer. PMID:35707004
Spatially resolved transcriptomics provide a new method for cancer research. PMID:35590346
Clinical and translational values of spatial transcriptomics. PMID:35365599
Statistical and machine learning methods for spatially resolved transcriptomics data analysis. PMID:35337374
Museum of spatial transcriptomics. PMID:35273392
Spatial components of molecular tissue biology. PMID:35132261
Computational elucidation of spatial gene expression variation from spatially resolved transcriptomics data. PMID:35036053
Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics. PMID:34145435
Review of multi-omics data resources and integrative analysis for human brain disorders. PMID:33969380
How to Use Online Tools to Generate New Hypotheses for Mammary Gland Biology Research: A Case Study for Wnt7b. PMID:33625717
A Picture Worth a Thousand Molecules-Integrative Technologies for Mapping Subcellular Molecular Organization and Plasticity in Developing Circuits. PMID:33469427
Stem Cells, Cell Therapies, and Bioengineering in Lung Biology and Disease 2019. PMID:33123557
Probing infectious disease by single-cell RNA sequencing: Progresses and perspectives. PMID:33106757
From whole-mount to single-cell spatial assessment of gene expression in 3D. PMID:33097816
Pinpointing Cell Identity in Time and Space. PMID:32923457
The 27th annual Nucleic Acids Research database issue and molecular biology database collection. PMID:31906604 - http://dx.doi.org/10.1093/nar/gkz934
Tags:
Tags
More detailed information about this field from each metasource.
gene expression data
metasource: Fairsharing.org
version: FAIRsharing.org: SpatialDB; A database for spatially resolved transcriptomes; DOI: https://doi.org/10.25504/FAIRsharing.0Hsbor; Last edited: Dec. 19, 2019, 11:06 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
gene functional annotation
metasource: Fairsharing.org
version: FAIRsharing.org: SpatialDB; A database for spatially resolved transcriptomes; DOI: https://doi.org/10.25504/FAIRsharing.0Hsbor; Last edited: Dec. 19, 2019, 11:06 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
tissue
metasource: Fairsharing.org
version: FAIRsharing.org: SpatialDB; A database for spatially resolved transcriptomes; DOI: https://doi.org/10.25504/FAIRsharing.0Hsbor; Last edited: Dec. 19, 2019, 11:06 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
nucleotide sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
transcriptional regulator sites and transcription factors
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
pathology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:27.619371
transcriptomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:27.619371
cell biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:27.619371
rna-seq
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:27.619371
Tags
More detailed information about this field from each metasource.
gene expression data
metasource: Fairsharing.orgversion: FAIRsharing.org: SpatialDB; A database for spatially resolved transcriptomes; DOI: https://doi.org/10.25504/FAIRsharing.0Hsbor; Last edited: Dec. 19, 2019, 11:06 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
gene functional annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: SpatialDB; A database for spatially resolved transcriptomes; DOI: https://doi.org/10.25504/FAIRsharing.0Hsbor; Last edited: Dec. 19, 2019, 11:06 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
tissue
metasource: Fairsharing.orgversion: FAIRsharing.org: SpatialDB; A database for spatially resolved transcriptomes; DOI: https://doi.org/10.25504/FAIRsharing.0Hsbor; Last edited: Dec. 19, 2019, 11:06 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
nucleotide sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
transcriptional regulator sites and transcription factors
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
pathology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:27.619371
transcriptomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:27.619371
cell biology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:27.619371
rna-seq
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:27.619371
gene expression gene functional annotation tissue nucleic acid sequence transcription pathology transcriptomics cell biology rna sequence
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