SNIC SUPR
Re-analysis of public single cell RNA-seq data from mouse
Dnr:

SNIC 2019/3-87

Type:

SNIC Medium Compute

Principal Investigator:

Oscar Franzén

Affiliation:

Karolinska Institutet

Start Date:

2019-02-27

End Date:

2020-03-01

Primary Classification:

30108: Cell and Molecular Biology

Allocation

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 single cell RNA sequencing studies. PanglaoDB contains pre-processed and pre-computed analyses from more than 871 single cell experiments covering most major single cell platforms and protocols, based on more than 3 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.