GEO DataSets

(Submitter supplied) Statins reduce cardiovascular disease risk by lowering plasma low density lipoprotein (LDL)-cholesterol. To identify novel pathways that modulate statin response, we assessed the influence of simvastatin exposure on expression quantitative trait locus (eQTL) associations across the genome in 480 lymphoblastoid cell lines (LCLs). Cell lines were derived blood samples collected ant entry visit from participants in the Cholesterol and Pharmacogenomics (CAP) trial, who underwent a 6 week 40mg/day simvastatin trial. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6883

960 Samples

Download data: TXT

(Submitter supplied) Most loci identified in genome wide association studies (GWAS) of complex traits reside in non-coding DNA and may contribute to phenotype via changes in gene regulation. The discovery of expression quantitative trait loci (?eQTLs?) can thus be used to more precisely identify modest but real disease associations and provide insights into their underlying molecular mechanisms. This is particularly true for analyses of expression in non-transformed cells from tissues relevant to the complex traits of interest. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6104

60 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; SNP genotyping by SNP array; Genome variation profiling by SNP array

Platforms:

GPL4133 GPL8887 GPL6104

748 Samples

Download data: TXT

(Submitter supplied) Most loci identified in genome wide association studies (GWAS) of complex traits reside in non-coding DNA and may contribute to phenotype via changes in gene regulation. The discovery of expression quantitative trait loci (‘eQTLs’) can thus be used to more precisely identify modest but real disease associations and provide insights into their underlying molecular mechanisms. This is particularly true for analyses of expression in non-transformed cells from tissues relevant to the complex traits of interest. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL8887

224 Samples

Download data: TXT

(Submitter supplied) Most loci identified in genome wide association studies (GWAS) of complex traits reside in non-coding DNA and may contribute to phenotype via changes in gene regulation. The discovery of expression quantitative trait loci (‘eQTLs’) can thus be used to more precisely identify modest but real disease associations and provide insights into their underlying molecular mechanisms. This is particularly true for analyses of expression in non-transformed cells from tissues relevant to the complex traits of interest. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

464 Samples

Download data: TXT

(Submitter supplied) Genetics of gene expression (eQTLs or expression QTLs) has proved an indispensable tool for understanding biological pathways and pathomechanisms of trait associated SNPs. However, power of most genome-wide eQTL studies is still limited. We performed a large eQTL study in peripheral blood mononuclear cells of 2,112 individuals increasing the power to detect trans-effects genome-wide. Going beyond univariate SNP-transcript associations, we analyse relations of eQTLs to biological pathways, polygenetic effects of expression regulation, trans-clusters, and enrichment of co-localised functional elements. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

2112 Samples

Download data: TXT

(Submitter supplied) Profiles of sequence variants that influence gene transcription are very important for understanding mechanisms that affect phenotypic variation and disease susceptibility. Using genotypes at 1.4 million SNPs and a comprehensive transcriptional profile of 15,454 coding genes and 6,113 lincRNA genes obtained from peripheral blood cells of 298 Japanese individuals, we mapped expression quantitative trait loci (eQTLs). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14550

301 Samples

Download data: TXT

(Submitter supplied) We performed promoter Capture Hi-C in HepG2 to investigate interactions between gene promoters and distal elements as a transcription-regulating mechanism contributing to these phenotypes. We also performed ChIP-Seq at 2h, 8h and 23h timepoints in HepG2 for Il1B treatment.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20301 GPL11154

10 Samples

Download data: BIGWIG, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL20301

54 Samples

Download data: BED

(Submitter supplied) RNA-seq was done on eight different lymphoblastoid cell lines for vehicle control, 3-MC agonist treatment and GNF-351 antagonist treatment for AHR to look at AHR regulated genes with different genetic backgrounds. We identified 69 genes that were highly differentially expressed after 3-MC or GNF-351 antagonist treatment with variation in the degree fo differential expression between the eight cell lines.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

48 Samples

Download data: TXT

(Submitter supplied) ChIP-seq was done on one lymphoblastoid cell lines for vehicle control, or 3-MC agonist treatment to identify AHR binding regions throughout the genome. We identified 17,688 common binding peaks between all ChIP treatments

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: BED

(Submitter supplied) The data set comprises individual array-based genome-wide gene expression data of 991 participants of the SHIP-TREND cohort generated using RNA prepared from whole blood. *** Due to privacy concerns, the SNP and phenotype data is not available with unrestricted access. Individuals wishing to obtain this data for research purposes may request access directly from the submitter (contact info below). ***

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

991 Samples

Download data: TXT

(Submitter supplied) Whole blood (paxgene) gene expression was measured using Affymetrix microarray from 377 individuals with rheumatoid arthritis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13158

377 Samples

Download data: CEL

(Submitter supplied) To explore the roles of cell-type specific methylation QTL (meQTL) for melanoma GWAS annotation, we generated DNA methylation data from the same sample set as our previouse eQTL study including 106 primary melanocyte cultures. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 480,000 CpGs in 106 primary melanocyte cultures. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13534

106 Samples

Download data: IDAT, TXT

(Submitter supplied) Prognostic biomarkers are useful to screen patients with clinically localized prostate cancer (PCa) who are at high risk of metastatic progression. The tumor transcriptome can be used to evaluate the aggressiveness of PCa and predict adverse patient outcomes. Genomewide gene expression levels were measured in primary tumor samples of 503 patients in a population‐based cohort.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14951

503 Samples

Download data: IDAT, TXT

(Submitter supplied) eQTL is a powerful method to detect genotype-expression correlation. To be able to identify the genes whose expression levels are correlated with germline genetic variants including the ones associated with melanoma, eQTL analysis was performed in 106 primary melanocyte cultrures

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array

Platform:

GPL22678

124 Samples

Download data: IDAT, TXT

(Submitter supplied) Maps of open chromatin in three primary human blood cell types of the myeloid lineage (megakaryocytes, erythroblasts and monocytes) using the formaldehyde-assisted isolation of regulatory elements method followed by next-generation sequencing (FAIRE-seq). We also generated FAIRE-seq data in the megakaryocytic cell line CHRF-288-11. In addition to our data sets, we retrieved FAIRE-seq data for the erythroblastoid cell line K562 (ENCODE Project Consortium 2012) and pancreatic islets (Gaulton et al. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL10999 GPL11154 GPL9115

6 Samples

Download data: BED

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; Expression profiling by array

Platforms:

GPL4133 GPL6801

128 Samples

Download data: CEL, CHP, TXT

(Submitter supplied) Elucidating the genetic basis underlying the variation in hepatic gene expression is of importance to understand disease etiology and drug metabolism variances. To date, no genome-wide eQTL analysis has been conducted in the Han Chinese, the largest ethnic group in the world. We performed a genome-wide eQTL mapping in a set of Han Chinese liver tissue (n=64).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

64 Samples

Download data: TXT

(Submitter supplied) Elucidating the genetic basis underlying the variation in hepatic gene expression is of importance to understand disease etiology and drug metabolism variances. To date, no genome-wide eQTL analysis has been conducted in the Han Chinese, the largest ethnic group in the world. We performed a genome-wide eQTL mapping in a set of Han Chinese liver tissue (n=64).

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL6801

64 Samples

Download data: CEL, CHP