Expression Atlas update: from tissues to single cells.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
08 01 2020
08 01 2020
Historique:
accepted:
16
10
2019
revised:
07
10
2019
received:
15
09
2019
pubmed:
31
10
2019
medline:
19
5
2020
entrez:
31
10
2019
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 31665515
pii: 5609521
doi: 10.1093/nar/gkz947
pmc: PMC7145605
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
D77-D83Subventions
Organisme : Wellcome Trust
ID : 108437/Z/15/Z
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 208391/Z/17/Z
Pays : United Kingdom
Informations de copyright
© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
Cell. 2015 May 21;161(5):1202-1214
pubmed: 26000488
Nucleic Acids Res. 2018 Jul 2;46(W1):W537-W544
pubmed: 29790989
Genome Biol. 2019 Mar 27;20(1):65
pubmed: 30917859
Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5
pubmed: 23193258
Nucleic Acids Res. 2019 Jan 8;47(D1):D1056-D1065
pubmed: 30462303
Nucleic Acids Res. 2019 Jan 8;47(D1):D442-D450
pubmed: 30395289
Plant J. 2017 Feb;89(4):789-804
pubmed: 27862469
Bioinformatics. 2010 Apr 15;26(8):1112-8
pubmed: 20200009
Nat Biotechnol. 2016 May;34(5):525-7
pubmed: 27043002
Nucleic Acids Res. 2019 Jan 8;47(D1):D711-D715
pubmed: 30357387
Nat Methods. 2013 Nov;10(11):1096-8
pubmed: 24056875
Genome Biol. 2018 Feb 6;19(1):15
pubmed: 29409532
Nucleic Acids Res. 2018 Jan 4;46(D1):D1181-D1189
pubmed: 29165610
Genome Biol. 2019 Mar 22;20(1):63
pubmed: 30902100
Nat Biotechnol. 2017 Apr 11;35(4):316-319
pubmed: 28398311
Nat Methods. 2018 Jul;15(7):475-476
pubmed: 29967506
Nucleic Acids Res. 2018 Jan 4;46(D1):D649-D655
pubmed: 29145629
Nucleic Acids Res. 2017 Jan 4;45(D1):D32-D36
pubmed: 27899630
Science. 2015 May 8;348(6235):648-60
pubmed: 25954001
Nat Commun. 2017 Jan 16;8:14049
pubmed: 28091601
Nucleic Acids Res. 2018 Jan 4;46(D1):D246-D251
pubmed: 29165655
Nucleic Acids Res. 2010 Jan;38(Database issue):D690-8
pubmed: 19906730