Expression Atlas update: from tissues to single cells

Author:

Papatheodorou Irene1,Moreno Pablo1ORCID,Manning Jonathan1,Fuentes Alfonso Muñoz-Pomer1,George Nancy1,Fexova Silvie1,Fonseca Nuno A1ORCID,Füllgrabe Anja1ORCID,Green Matthew1,Huang Ni12,Huerta Laura1,Iqbal Haider1,Jianu Monica1,Mohammed Suhaib1,Zhao Lingyun1,Jarnuczak Andrew F1,Jupp Simon1ORCID,Marioni John123ORCID,Meyer Kerstin2,Petryszak Robert1,Prada Medina Cesar Augusto1,Talavera-López Carlos2,Teichmann Sarah2,Vizcaino Juan Antonio1ORCID,Brazma Alvis1

Affiliation:

1. European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK

2. Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK

3. Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK

Abstract

Abstract Expression Atlas is EMBL-EBI’s resource for gene and protein expression. It sources and compiles data on the abundance and localisation of RNA and proteins in various biological systems and contexts and provides open access to this data for the research community. With the increased availability of single cell RNA-Seq datasets in the public archives, we have now extended Expression Atlas with a new added-value service to display gene expression in single cells. Single Cell Expression Atlas was launched in 2018 and currently includes 123 single cell RNA-Seq studies from 12 species. The website can be searched by genes within or across species to reveal experiments, tissues and cell types where this gene is expressed or under which conditions it is a marker gene. Within each study, cells can be visualized using a pre-calculated t-SNE plot and can be coloured by different features or by cell clusters based on gene expression. Within each experiment, there are links to downloadable files, such as RNA quantification matrices, clustering results, reports on protocols and associated metadata, such as assigned cell types.

Funder

European Molecular Biology Laboratory

Wellcome Trust

National Science Foundation

BBSRC

Publisher

Oxford University Press (OUP)

Subject

Genetics

Reference22 articles.

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