PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data

• Published in: Database : the journal of biological databases and curation Vol. 2019
• Main Authors: Franzén, Oscar, Gan, Li-Ming, Björkegren, Johan L M
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 2019
• Subjects: Animals; Bioinformatik och systembiologi (metodutveckling under 10203); Biologi (Medicinska tillämpningar under 3 och lantbruksvetenskapliga under 4); Cell- och molekylärbiologi; Databases, Nucleic Acid; Evolutionsbiologi; Humans; Medicin och hälsovetenskap; Medicinska och farmaceutiska grundvetenskaper; Mice; Naturvetenskap; Original; RNA - biosynthesis; RNA - genetics; RNA-Seq
• ISSN: 1758-0463; 1758-0463
• DOI: 10.1093/database/baz046

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.