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Protocols

EGA specifications

Information


Unique identifier OMICS_01028
Name EGA
Alternative name European Genome-phenome Archive
Restrictions to use None
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline EGA

Publication for European Genome-phenome Archive

EGA citations

 (30)
library_books

H3Africa: current perspectives

2018
PMCID: 5903476
PMID: 29692621
DOI: 10.2147/PGPM.S141546

[…] d sequencing, and data from genotyping or copy number variant arrays. The data constitute a valuable resource for disease studies in Africa and are being submitted to public repositories, such as the European Genome–Phenome Archive (EGA) and the European Nucleotide Archive (ENA). In order to ensure timely deposition of the data into the public domain and responsible sharing of the data, the H3Afri […]

call_split

DNA methylation as a mediator of the association between prenatal adversity and risk factors for metabolic disease in adulthood

2018
Sci Adv
PMCID: 5792223
PMID: 29399631
DOI: 10.1126/sciadv.aao4364
call_split See protocol

[…] h gene expression and validate associations with BMI or TG, we referred to the DNAm data of 3296 individuals () measured within the Genome of the Netherlands reference project [GoNL; deposited at the European Genome-phenome Archive (EGA) under accession number EGAC00001000277]. Preprocessing and normalization were done as described above for both data sets. R Code for the quality control and norma […]

library_books

Punctuated evolution of canonical genomic aberrations in uveal melanoma

2018
Nat Commun
PMCID: 5760704
PMID: 29317634
DOI: 10.1038/s41467-017-02428-w

[…] Raw data files from 80 TCGA UM samples was obtained from the Cancer Genomics Hub (CGHub). Raw data files from the Martin et al. and Furney et al. raw data were obtained from the European Genome-phenome Archive (EGA). Data sets provided in BAM format (TCGA; Furney et al.) were converted back into FASTQ files using bamUtil:bam2FastQ (v1.0.13) and were adjusted into proper forma […]

library_books

A lost opportunity for science: journals promote data sharing in metabolomics but do not enforce it

2017
Metabolomics
PMCID: 5808091
PMID: 29479297
DOI: 10.1007/s11306-017-1309-5

[…] atients with the same disease. There is a far greater risk of patient identification from genetic data than metabolomic. Despite this, a repository for sensitive genomics data has been developed, the European Genome-phenome Archive (EGA) (Lappalainen et al. ), which allows controlled access to datasets that cannot be made publically available. A similar repository could be established for clinical […]

library_books

Transcriptome evolution from breast epithelial cells to basal like tumors

2017
Oncotarget
PMCID: 5787480
PMID: 29416627
DOI: 10.18632/oncotarget.23065

[…] All together 1,988 cancer samples measured by Illumina gene chips published in the Metabric project were obtained from the European Genome-phenome Archive (EGA) (https://www.ebi.ac.uk/ega/) []. As a substitute of using the processed dataset, the entire dataset including each individual arrays was re-processed. In this, th […]

library_books

PD 1 is a haploinsufficient suppressor of T cell lymphomagenesis

2017
Nature
PMCID: 5821214
PMID: 29143824
DOI: 10.1038/nature24649

[…] le nucleotide variants, small indels, and copy number aberrations (CNAs) that affect the PDCD1 locus. Whole-genome sequencing data (aligned BAM files, 47 tumour-normal pairs) were downloaded from the European Genome-phenome Archive with permission. Whole exome sequencing data (aligned BAM files, 34 tumour-normal pairs) were downloaded from the Sequence Read Archive (accession PRJNA285408). The BAM […]

Citations

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EGA institution(s)
European Molecular Biology Laboratory–European Bioinformatics Institute, Hinxton, UK; Centre for Genomic Regulation, Barcelona, Spain; Institute of Evolutionary Biology, Universitat Pompeu Fabra–Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain

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