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. 2020 Jan 8;48(D1):D77-D83.
doi: 10.1093/nar/gkz947.

Expression Atlas Update: From Tissues to Single Cells

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Free PMC article

Expression Atlas Update: From Tissues to Single Cells

Irene Papatheodorou et al. Nucleic Acids Res. .
Free PMC article

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.

Figures

Figure 1.
Figure 1.
Screenshot of the ‘Browse Experiments’ page. A user can search through the experiments by species or other keywords, quickly link to their results pages or download raw, normalized data and metadata bundles from one or more studies.
Figure 2.
Figure 2.
Search results for gene ASPM, filtered to show datasets where ASPM is expressed in Mus musculus.
Figure 3.
Figure 3.
The experimental results of the ‘Single cell transcriptome of the human pancreas’ as shown in https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-81547/results/tsne?geneId=ENSG00000172023&colourBy=metadata&metadata=inferred_cell_type The results are presented by two identical t-SNE plots where cells are coloured by ‘inferred cell type’ values on the left and the expression levels of gene REG1B (ENSG00000172023) on the right. By viewing these results side by side, a user can easily infer that REG1B is primarily expressed in pancreatic acinar cells.
Figure 4.
Figure 4.
Screenshot of a heatmap showing the average expression of ‘marker genes’ within each cell cluster of a single study as shown in https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-81547/results/tsne?geneId=ENSG00000172023&colourBy=metadata&metadata=inferred_cell_type&markerGeneK=10.

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References

    1. Kapushesky M., Emam I., Holloway E., Kurnosov P., Zorin A., Malone J., Rustici G., Williams E., Parkinson H., Brazma A. Gene expression atlas at the european bioinformatics institute. Nucleic Acids Res. 2010; 38:D690–D698. - PMC - PubMed
    1. Athar A., Fullgrabe A., George N., Iqbal H., Huerta L., Ali A., Snow C., Fonseca N.A., Petryszak R., Papatheodorou I. et al. . ArrayExpress update—from bulk to single-cell expression data. Nucleic Acids Res. 2019; 47:D711–D715. - PMC - PubMed
    1. Barrett T., Wilhite S.E., Ledoux P., Evangelista C., Kim I.F., Tomashevsky M., Marshall K.A., Phillippy K.H., Sherman P.M., Holko M. et al. . NCBI GEO: archive for functional genomics data sets–update. Nucleic Acids Res. 2013; 41:D991–D995. - PMC - PubMed
    1. Toribio A.L., Alako B., Amid C., Cerdeño-Tarrága A., Clarke L., Cleland I., Fairley S., Gibson R., Goodgame N., Ten Hoopen P. et al. . European Nucleotide Archive in 2016. Nucleic Acids Res. 2017; 45:D32–D36. - PMC - PubMed
    1. Tello-Ruiz M., Naithani S., Stein J., Gupta P., Campbell M., Olson A., Wei S., Preece J., Geniza M.J., Jiao Y. et al. . Gramene 2018: unifying comparative genomics and pathway resources for plant research. Nucleic Acids Res. 2017; 46:D1181–D1189. - PMC - PubMed

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