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GNomEx specifications


Unique identifier OMICS_01005
Name GNomEx
Alternative name Genomic Experiment Data Repository and Core LIMS
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Database management system MySQL
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


Publication for Genomic Experiment Data Repository and Core LIMS

GNomEx citations


Rapid clinical diagnostic variant investigation of genomic patient sequencing data with iobio web tools

PMCID: 5915807
PMID: 29707261
DOI: 10.1017/cts.2017.311

[…] (e.g., genes), and must either be accessible as a URL, or be stored locally on the clinician’s own computer. The “Files” tab in gene.iobio provides the interface to select the files for analysis. The GNomEx [] genomic data LIMS at the our institution simplifies this process by providing clickable links for our physician/analysts to commence analysis on a given patient. Similar integration at the r […]


A CRISPR screen identifies genes controlling Etv2 threshold expression in murine hemangiogenic fate commitment

Nat Commun
PMCID: 5599515
PMID: 28912455
DOI: 10.1038/s41467-017-00667-5
call_split See protocol

[…] E57409 (sample “ES” and “EpiSC”), GSE36114 (sample “endo_d6”, representing ES cell for endoderm differentiation on day 6), GSE69080 (“mes”, “hb”, “hp”), GSE55310 (“he”), 7R2 (, sample “cp”, representing ES cells differentiated to cardiac progenitors). The RNA-seq data have been deposited in the NCBI Gene Expression Omnibus (GEO) database under accession code GSE8564 […]


VEGF amplifies transcription through ETS1 acetylation to enable angiogenesis

Nat Commun
PMCID: 5575285
PMID: 28851877
DOI: 10.1038/s41467-017-00405-x

[…] High throughput data are available on the Cardiovascular Development Consortium server at ChIP-Seq and RNA-Seq data have also been deposited at GEO under accession code GSE93030. […]


Mapping cell type specific transcriptional enhancers using high affinity, lineage specific Ep300 bioChIP seq

PMCID: 5295818
PMID: 28121289
DOI: 10.7554/eLife.22039.038

[…] pe E12.5 ventricular cardiomyocytes. These data are available via the Gene Expression Omnibus (accession number GSE88789) or the Cardiovascular Development Consortium server (; login as guest).The following public data sources were used for this study: ES_Ep300_ChIP, GSE36027; ES_Ep300_input, GSE36027; E12.5_Histone_input, GSE82850, E12.5_H3K27ac, GSE82449; E12.5_H3 […]


Transcriptional Profiling of Cultured, Embryonic Epicardial Cells Identifies Novel Genes and Signaling Pathways Regulated by TGFβR3 In Vitro

PLoS One
PMCID: 4978490
PMID: 27505173
DOI: 10.1371/journal.pone.0159710
call_split See protocol

[…] ion profiles were generated as described [] using a Bayesian p-value ( and Figs). Data deposited at the Cardiovascular Development Consortium (CvDC) Data Repository (, external experiment number 38R1 ( […]


Comprehensive analysis of promoter proximal RNA polymerase II pausing across mammalian cell types

Genome Biol
PMCID: 4893286
PMID: 27259512
DOI: 10.1186/s13059-016-0984-2

[…] ries were sequenced on a HiSeq2500 (Illumina; 50 nt single end sequencing). The data are available from GEO GSE60872 or from the Cardiovascular Development Consortium server (; sign in as guest). […]


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GNomEx institution(s)
Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, USA; Research Informatics, Huntsman Cancer Institute, Salt Lake City, USA; Microarray/Next Generation Sequencing Shared Resource, Huntsman Cancer Institute, Salt Lake City, USA; Bioinformatics Shared Resource, University of Utah, Huntsman Cancer Institute, Salt Lake City, USA

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