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GSE48152
Homo sapiens
705 Downloadable Samples
Illumina HumanHT-12 V3.0 expression beadchip
Description
The identification of multiple signals at individual loci could explain additional phenotypic variance ('missing heritability') of common traits, and help identify causal genes. We examined gene expression levels as a model trait because of the large number of strong genetic effects acting in cis. Using expression profiles from 613 individuals, we performed genome-wide single nucleotide polymorphism (SNP) analyses to identify cis-expression quantitative trait loci (eQTLs), and conditional analysis to identify second signals. We examined patterns of association when accounting for multiple SNPs at a locus and when including additional SNPs from the 1000 Genomes Project. We identified 1298 cis-eQTLs at an approximate false discovery rate 0.01, of which 118 (9%) showed evidence of a second independent signal. For this subset of 118 traits, accounting for two signals resulted in an average 31% increase in phenotypic variance explained (Wilcoxon P< 0.0001). The association of SNPs with cis gene expression could increase, stay similar or decrease in significance when accounting for linkage disequilibrium with second signals at the same locus. Pairs of SNPs increasing in significance tended to have gene expression increasing alleles on opposite haplotypes, whereas pairs of SNPs decreasing in significance tended to have gene expression increasing alleles on the same haplotypes. Adding data from the 1000 Genomes Project showed that apparently independent signals could be potentially explained by a single association signal. Our results show that accounting for multiple variants at a locus will increase the variance explained in a substantial fraction of loci, but that allelic heterogeneity will be difficult to define without resequencing loci and functional work.
Publication Title
Allelic heterogeneity and more detailed analyses of known loci explain additional phenotypic variation and reveal complex patterns of association.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 350 Downloadable Samples
Illumina HumanHT-12 V3.0 expression beadchip, Illumina HumanHT-12 V4.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Systematic identification of trans eQTLs as putative drivers of known disease associations.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 228 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip, Illumina HumanHT-12 V3.0 expression beadchip
Description
Samples were collected from 'control participants' of the Heart and Vascular Health (HVH) study that constitutes a group of population based case control studies of myocardial infarction (MI), stroke, venous thromboembolism (VTE), and atrial fibrillation (AF) conducted among 30-79 year old members of Group Health, a large integrated health care organization in Washington State.
Publication Title
Systematic identification of trans eQTLs as putative drivers of known disease associations.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 122 Downloadable Samples
- Illumina HumanHT-12 V3.0 expression beadchip
Description
Samples were collected from 'control participants' of the Heart and Vascular Health (HVH) study that constitutes a group of population based case control studies of myocardial infarction (MI), stroke, venous thromboembolism (VTE), and atrial fibrillation (AF) conducted among 30-79 year old members of Group Health, a large integrated health care organization in Washington State.
Publication Title
Systematic identification of trans eQTLs as putative drivers of known disease associations.
Sample Metadata Fields
Sex, Specimen part
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
The embryo lethal adenosine methylase tDNA knockout line SALK_074069 was partially complemented with its cDNA driven by the embryo specific ABI3 promoter (A6 lines). The plants have reduced adenosine methylation and show pleiotropic phenotypes. Rosette leaves were harvested from 3 week old plants, both wild-type and mutant plants in triplicate and analysed using the Affymetrix ATH1 array.
Publication Title
Adenosine Methylation in Arabidopsis mRNA is Associated with the 3' End and Reduced Levels Cause Developmental Defects.
Sample Metadata Fields
Age, Specimen part
View Samples- Drosophila melanogaster
- 6 Downloadable Samples
Illumina HiSeq 2500
Description
Methylation of mRNA at the N6 position of adenosin is known for a long time, but its function remains poorly understood. Here generated a null mutant in the catalytic subunit of the m6A mRNA methylosome, dIME4, in Drosophila to determine the impact of loss of m6A on gene expression using Illumina sequencing. Overall design: Since dIME4 is preferentially expressed in the nervous system and dIME4 null mutants are viable, we compared gene expression and alternative splicing in wild type (2 samples) and dIME4 mutants (3 samples) with genetic background matched w control females in neuron enriched head/thorax.
Publication Title
m<sup>6</sup>A potentiates Sxl alternative pre-mRNA splicing for robust Drosophila sex determination.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Drosophila melanogaster
- 5 Downloadable Samples
- Illumina HiSeq 2500
Description
Methylation of mRNA at the N6 position of adenosin is known for a long time, but its function remains poorly understood. Here generated a null mutant in the catalytic subunit of the m6A mRNA methylosome, dIME4, in Drosophila to determine the impact of loss of m6A on gene expression using Illumina sequencing. Overall design: Since dIME4 is preferentially expressed in the nervous system and dIME4 null mutants are viable, we compared gene expression and alternative splicing in wild type (2 samples) and dIME4 mutants (3 samples) with genetic background matched w control females in neuron enriched head/thorax.
Publication Title
m<sup>6</sup>A potentiates Sxl alternative pre-mRNA splicing for robust Drosophila sex determination.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 22 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Analysis of the transcriptome of mononuclear side population (SP) and main population (MP) cells of human fetal skeletal muscle from 12 human subjects of gestational age 14-18 weeks.
Publication Title
Regulation of myogenic progenitor proliferation in human fetal skeletal muscle by BMP4 and its antagonist Gremlin.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Functional analysis of ABCB5 in A375 and G3361 melanoma cells, by comparing stably-transfected controls to ABCB5-shRNA-targeted cells.
Publication Title
ABCB5 maintains melanoma-initiating cells through a proinflammatory cytokine signaling circuit.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
To find BMAL1-regulated genes in mice pituitary gland we performed a differential microarray from wild-type vs Bmal1-/- knock-out mice
Publication Title
Chromatin remodeling as a mechanism for circadian prolactin transcription: rhythmic NONO and SFPQ recruitment to HLTF.
Sample Metadata Fields
Sex, Specimen part
View Samples