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

TLDR

Single‑cell RNA sequencing is widely used to map gene expression at the cellular level, yet most datasets are deposited as raw data, making them difficult for biologists to access without complex computational pipelines. The authors created PanglaoDB, an online database with a user‑friendly interface for exploring published mouse and human single‑cell RNA‑seq studies. PanglaoDB aggregates pre‑processed data from over 1,054 experiments (4 million+ cells) across many platforms, provides an interface to query cell types, pathways, and networks, and includes a community‑curated marker compendium of >6,000 gene‑cell‑type associations. The resource includes a community‑curated marker compendium of over 6,000 gene‑cell‑type associations, enabling automatic cell‑type annotation.

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.