Abstract
Single-cell RNA sequencing is an increasingly used method to measure gene expression at the single cell level and build cell-type atlases of tissues. Hundreds of single-cell sequencing datasets have already been published. However, studies are frequently deposited as raw data, a format difficult to access for biological researchers due to the need for data processing using complex computational pipelines. We have implemented an online database, PanglaoDB, accessible through a user-friendly interface that can be used to explore published mouse and human single cell RNA sequencing studies. PanglaoDB contains pre-processed and pre-computed analyses from more than 1054 single-cell experiments covering most major single cell platforms and protocols, based on more than 4 million cells from a wide range of tissues and organs. The online interface allows users to query and explore cell types, genetic pathways and regulatory networks. In addition, we have established a community-curated cell-type marker compendium, containing more than 6000 gene-cell-type associations, as a resource for automatic annotation of cell types.
Keywords
Computer scienceAnnotationCell typeComputational biologyCompendiumCellSingle-cell analysisWeb serverWorld Wide WebBiologyThe InternetGeneticsArtificial intelligence
MeSH Terms
AnimalsDatabasesNucleic AcidHumansMiceRNARNA-Seq
Affiliated Institutions
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Publication Info
- Year
- 2019
- Type
- article
- Volume
- 2019
- Citations
- 1495
- Access
- Closed
External Links
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Cite This
Oscar Franzén,
Li‐Ming Gan,
Johan Björkegren
(2019).
PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.
Database
, 2019
.
https://doi.org/10.1093/database/baz046
Identifiers
- DOI
- 10.1093/database/baz046
- PMID
- 30951143
- PMCID
- PMC6450036