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Expression Atlas update: from tissues to single cells

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...

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Autores principales: Papatheodorou, Irene, Moreno, Pablo, Manning, Jonathan, Fuentes, Alfonso Muñoz-Pomer, George, Nancy, Fexova, Silvie, Fonseca, Nuno A, Füllgrabe, Anja, Green, Matthew, Huang, Ni, Huerta, Laura, Iqbal, Haider, Jianu, Monica, Mohammed, Suhaib, Zhao, Lingyun, Jarnuczak, Andrew F, Jupp, Simon, Marioni, John, Meyer, Kerstin, Petryszak, Robert, Prada Medina, Cesar Augusto, Talavera-López, Carlos, Teichmann, Sarah, Vizcaino, Juan Antonio, Brazma, Alvis
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145605/
https://www.ncbi.nlm.nih.gov/pubmed/31665515
http://dx.doi.org/10.1093/nar/gkz947
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author Papatheodorou, Irene
Moreno, Pablo
Manning, Jonathan
Fuentes, Alfonso Muñoz-Pomer
George, Nancy
Fexova, Silvie
Fonseca, Nuno A
Füllgrabe, Anja
Green, Matthew
Huang, Ni
Huerta, Laura
Iqbal, Haider
Jianu, Monica
Mohammed, Suhaib
Zhao, Lingyun
Jarnuczak, Andrew F
Jupp, Simon
Marioni, John
Meyer, Kerstin
Petryszak, Robert
Prada Medina, Cesar Augusto
Talavera-López, Carlos
Teichmann, Sarah
Vizcaino, Juan Antonio
Brazma, Alvis
author_facet Papatheodorou, Irene
Moreno, Pablo
Manning, Jonathan
Fuentes, Alfonso Muñoz-Pomer
George, Nancy
Fexova, Silvie
Fonseca, Nuno A
Füllgrabe, Anja
Green, Matthew
Huang, Ni
Huerta, Laura
Iqbal, Haider
Jianu, Monica
Mohammed, Suhaib
Zhao, Lingyun
Jarnuczak, Andrew F
Jupp, Simon
Marioni, John
Meyer, Kerstin
Petryszak, Robert
Prada Medina, Cesar Augusto
Talavera-López, Carlos
Teichmann, Sarah
Vizcaino, Juan Antonio
Brazma, Alvis
author_sort Papatheodorou, Irene
collection PubMed
description 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.
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spelling pubmed-71456052020-04-13 Expression Atlas update: from tissues to single cells Papatheodorou, Irene Moreno, Pablo Manning, Jonathan Fuentes, Alfonso Muñoz-Pomer George, Nancy Fexova, Silvie Fonseca, Nuno A Füllgrabe, Anja Green, Matthew Huang, Ni Huerta, Laura Iqbal, Haider Jianu, Monica Mohammed, Suhaib Zhao, Lingyun Jarnuczak, Andrew F Jupp, Simon Marioni, John Meyer, Kerstin Petryszak, Robert Prada Medina, Cesar Augusto Talavera-López, Carlos Teichmann, Sarah Vizcaino, Juan Antonio Brazma, Alvis Nucleic Acids Res Database Issue 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. Oxford University Press 2020-01-08 2019-10-30 /pmc/articles/PMC7145605/ /pubmed/31665515 http://dx.doi.org/10.1093/nar/gkz947 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Issue
Papatheodorou, Irene
Moreno, Pablo
Manning, Jonathan
Fuentes, Alfonso Muñoz-Pomer
George, Nancy
Fexova, Silvie
Fonseca, Nuno A
Füllgrabe, Anja
Green, Matthew
Huang, Ni
Huerta, Laura
Iqbal, Haider
Jianu, Monica
Mohammed, Suhaib
Zhao, Lingyun
Jarnuczak, Andrew F
Jupp, Simon
Marioni, John
Meyer, Kerstin
Petryszak, Robert
Prada Medina, Cesar Augusto
Talavera-López, Carlos
Teichmann, Sarah
Vizcaino, Juan Antonio
Brazma, Alvis
Expression Atlas update: from tissues to single cells
title Expression Atlas update: from tissues to single cells
title_full Expression Atlas update: from tissues to single cells
title_fullStr Expression Atlas update: from tissues to single cells
title_full_unstemmed Expression Atlas update: from tissues to single cells
title_short Expression Atlas update: from tissues to single cells
title_sort expression atlas update: from tissues to single cells
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145605/
https://www.ncbi.nlm.nih.gov/pubmed/31665515
http://dx.doi.org/10.1093/nar/gkz947
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