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SCPortalen: human and mouse single-cell centric database.

Imad Abugessaisa1, Shuhei Noguchi1, Michael Böttcher1

  • 1Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Yokohama, Kanagawa 230-0045, Japan.

Nucleic Acids Research
|October 19, 2017
PubMed
Summary
This summary is machine-generated.

SCPortalen is a new database that makes diverse single-cell transcriptomics data comparable and reusable. It provides curated, analyzed datasets for researchers studying cell types and heterogeneity.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Cell Biology

Background:

  • Published single-cell datasets are valuable but challenging to integrate due to varying protocols and analyses.
  • Reconciling diverse single-cell data is crucial for broader scientific discovery.

Purpose of the Study:

  • To develop a centralized, user-friendly database for accessing and analyzing single-cell transcriptomics data.
  • To enhance the reusability and comparability of large-scale single-cell datasets.

Main Methods:

  • Manual curation of metadata and annotation with standard ontology terms.
  • Standardized quality assessment and primary data processing using a dedicated pipeline.
  • Integration of transcriptomics data with available single-cell image files.

Main Results:

  • SCPortalen provides access to human and mouse single-cell transcriptomics datasets from INSDC.
  • The database ensures data quality through rigorous assessment and standardized analysis.
  • Users can easily search, explore, and download datasets via a web interface.

Conclusions:

  • SCPortalen facilitates novel research by making diverse single-cell data accessible and comparable.
  • The database supports researchers investigating specific cell types and population heterogeneity.
  • It serves as a valuable resource for the broader scientific community interested in single-cell biology.