SCPortalen
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SCPortalen is a single-cell database created to facilitate and enable researchers to access and explore published single-cell datasets. It integrates human and mouse single-cell transcriptomics datasets, single-cell metadata, cell images and sequence information.
Description
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SCPortalen is a single-cell database created to facilitate and enable researchers to access and explore published single-cell datasets. It integrates human and mouse single-cell transcriptomics datasets, single-cell metadata, cell images and sequence information.
metasource: Fairsharing.orgversion: FAIRsharing.org: SCPortalen; SCPortalen; DOI: https://doi.org/10.25504/FAIRsharing.wFo3UE; Last edited: Feb. 13, 2020, 1:34 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Published single-cell datasets are rich resources for investigators who want to address questions not originally asked by the creators of the datasets. The single-cell datasets might be obtained by different protocols and diverse analysis strategies. The main challenge in utilizing such single-cell data is how we can make the various large-scale datasets to be comparable and reusable in a different context. To challenge this issue, we developed the single-cell centric database ‘SCPortalen’. The current version of the database covers human and mouse single-cell transcriptomics datasets that are publicly available from the INSDC sites. The original metadata was manually curated and single-cell samples were annotated with standard ontology terms. Following that, common quality assessment procedures were conducted to check the quality of the raw sequence. Furthermore, primary data processing of the raw data followed by advanced analyses and interpretation have been performed from scratch using our pipeline. In addition to the transcriptomics data, SCPortalen provides access to single-cell image files whenever available.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://single-cell.clst.riken.jp/Webpage
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http://single-cell.clst.riken.jp/
metasource: Fairsharing.orgversion: FAIRsharing.org: SCPortalen; SCPortalen; DOI: https://doi.org/10.25504/FAIRsharing.wFo3UE; Last edited: Feb. 13, 2020, 1:34 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Licence:
Name: Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain DedicationLicence name
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Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
metasource: Fairsharing.orgversion: FAIRsharing.org: SCPortalen; SCPortalen; DOI: https://doi.org/10.25504/FAIRsharing.wFo3UE; Last edited: Feb. 13, 2020, 1:34 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Licence URL
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https://creativecommons.org/publicdomain/zero/1.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: SCPortalen; SCPortalen; DOI: https://doi.org/10.25504/FAIRsharing.wFo3UE; Last edited: Feb. 13, 2020, 1:34 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Publications:
Publications
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SCPortalen: human and mouse single-cell centric database
PMID: 29045713
metasource: Fairsharing.org
version: FAIRsharing.org: SCPortalen; SCPortalen; DOI: https://doi.org/10.25504/FAIRsharing.wFo3UE; Last edited: Feb. 13, 2020, 1:34 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/gkx949
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.
SCPortalen: human and mouse single-cell centric database
PMID: 29045713
metasource: Fairsharing.org
version: FAIRsharing.org: SCPortalen; SCPortalen; DOI: https://doi.org/10.25504/FAIRsharing.wFo3UE; Last edited: Feb. 13, 2020, 1:34 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/gkx949
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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SCPortalen: human and mouse single-cell centric database
PubMed citations: 15.
15 articles citing: SCPortalen: human and mouse single-cell centric database
scINSIGHT for interpreting single-cell gene expression from biologically heterogeneous data. PMID:35313930
SkewC: Identifying cells with skewed gene body coverage in single-cell RNA sequencing data. PMID:35146392
Diagnostic Evidence GAuge of Single cells (DEGAS): a flexible deep transfer learning framework for prioritizing cells in relation to disease. PMID:35105355
Single-cell mapper (scMappR): using scRNA-seq to infer the cell-type specificities of differentially expressed genes. PMID:33655208
LnCeCell: a comprehensive database of predicted lncRNA-associated ceRNA networks at single-cell resolution. PMID:33219686
TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment. PMID:33179754
SC2disease: a manually curated database of single-cell transcriptome for human diseases. PMID:33010177
Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST. PMID:32651388
A Single Cell but Many Different Transcripts: A Journey into the World of Long Non-Coding RNAs. PMID:31906285
SCDevDB: A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes. PMID:31611909
A statistical simulator scDesign for rational scRNA-seq experimental design. PMID:31510652
PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data. PMID:30951143
C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution. PMID:30664627
CancerSEA: a cancer single-cell state atlas. PMID:30329142
The 2018 Nucleic Acids Research database issue and the online molecular biology database collection. PMID:29316735 - http://dx.doi.org/10.1093/nar/gkx949
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cell
metasource: Fairsharing.org
version: FAIRsharing.org: SCPortalen; SCPortalen; DOI: https://doi.org/10.25504/FAIRsharing.wFo3UE; Last edited: Feb. 13, 2020, 1:34 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
cellular assay
metasource: Fairsharing.org
version: FAIRsharing.org: SCPortalen; SCPortalen; DOI: https://doi.org/10.25504/FAIRsharing.wFo3UE; Last edited: Feb. 13, 2020, 1:34 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
image
metasource: Fairsharing.org
version: FAIRsharing.org: SCPortalen; SCPortalen; DOI: https://doi.org/10.25504/FAIRsharing.wFo3UE; Last edited: Feb. 13, 2020, 1:34 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
sequencing
metasource: Fairsharing.org
version: FAIRsharing.org: SCPortalen; SCPortalen; DOI: https://doi.org/10.25504/FAIRsharing.wFo3UE; Last edited: Feb. 13, 2020, 1:34 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
region
metasource: Fairsharing.org
version: FAIRsharing.org: SCPortalen; SCPortalen; DOI: https://doi.org/10.25504/FAIRsharing.wFo3UE; Last edited: Feb. 13, 2020, 1:34 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Tags
More detailed information about this field from each metasource.
cell
metasource: Fairsharing.orgversion: FAIRsharing.org: SCPortalen; SCPortalen; DOI: https://doi.org/10.25504/FAIRsharing.wFo3UE; Last edited: Feb. 13, 2020, 1:34 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
cellular assay
metasource: Fairsharing.orgversion: FAIRsharing.org: SCPortalen; SCPortalen; DOI: https://doi.org/10.25504/FAIRsharing.wFo3UE; Last edited: Feb. 13, 2020, 1:34 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
image
metasource: Fairsharing.orgversion: FAIRsharing.org: SCPortalen; SCPortalen; DOI: https://doi.org/10.25504/FAIRsharing.wFo3UE; Last edited: Feb. 13, 2020, 1:34 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
sequencing
metasource: Fairsharing.orgversion: FAIRsharing.org: SCPortalen; SCPortalen; DOI: https://doi.org/10.25504/FAIRsharing.wFo3UE; Last edited: Feb. 13, 2020, 1:34 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
region
metasource: Fairsharing.orgversion: FAIRsharing.org: SCPortalen; SCPortalen; DOI: https://doi.org/10.25504/FAIRsharing.wFo3UE; Last edited: Feb. 13, 2020, 1:34 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
cell cellular assay sequencing region
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