GEO DataSets

(Submitter supplied) Edited mendelian disease SNP rs199643834 responsible for Birt-Hogg-Dubé Syndrome into 293T cells using CRISPR/Cas9

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

13 Samples

Download data: TXT

(Submitter supplied) Analysis of expression quantitative trait loci (eQTLs) using RNA derived from freshly harvested peripheral blood CD4+ lymphocytes from 200 asthmatics collected in clinical settings.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6104

200 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Expression profiling by array

Platforms:

GPL6801 GPL6947

70 Samples

Download data: CEL

(Submitter supplied) Introduction: Cis-acting regulatory single nucleotide polymorphisms (SNPs) at specific loci may modulate penetrance of germline mutations at the same loci by introducing different levels of expression of the wild-type allele. We have previously reported that BRCA2 shows differential allelic expression and we hypothesize that the known variable penetrance of BRCA2 mutations might be associated with this mechanism. more...

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array

Platform:

GPL6801

37 Samples

Download data: CEL

(Submitter supplied) Introduction: Cis-acting regulatory single nucleotide polymorphisms (SNPs) at specific loci may modulate penetrance of germline mutations at the same loci by introducing different levels of expression of the wild-type allele. We have previously reported that BRCA2 shows differential allelic expression and we hypothesize that the known variable penetrance of BRCA2 mutations might be associated with this mechanism. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

33 Samples

Download data: TXT

(Submitter supplied) Genome-wide association studies (GWAS) have identified genomic loci associated with complex diseases but mechanistic insights are impeded by the lack of understanding of how specific risk variants functionally contribute to diseases. Here we describe an experimental strategy to robustly identify cis-acting effects of genetic variants in regulatory elements on gene expression by combining genome-wide epigenetic information with CRISPR/Cas genome editing in human pluripotent cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

11 Samples

Download data: WIG

(Submitter supplied) Identification of causal variants and mechanisms underlying complex disease traits in humans requires strategies to locate and fine-map functional regulatory variants in disease-relevant cell types. To discover functional regulatory variants in primary aortic endothelial cells (ECs) from humans, we collected genetic, transcriptomic, and four epigenomic phenotypes in a population of up to 150 human donors representing individuals of both sexes and three major ancestries. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL20301

504 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

705 Samples

Download data: TXT

(Submitter supplied) We have combined high-quality genome sequencing and RNA-sequencing data within a 17-individual, three generation family. Using these data, we have contrasted cis-acting expression, allele-specific expression and splicing quantitative trait loci (collectively termed eQTLs) within the family to eQTLs discovered within a cell-type and ethnicity-matched population sample. We identified that eQTL that exhibit larger effects in the family compared to the population are enriched for rare regulatory and splicing variants and were more likely to influence essential genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

17 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:

GPL13135 GPL16110 GPL6244

372 Samples

Download data: CEL

(Submitter supplied) Genome-wide association studies (GWAS) have been pivotal to increasing our understanding of intestinal disease. However, the mode by which genetic variation results in phenotypic change remains largely unknown, with many associated polymorphisms likely to modulate gene expression. Analyses of expression quantitative trait loci (eQTL) to date indicate that as many as 50% of these are tissue specific. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL13135 GPL16110

173 Samples

Download data

(Submitter supplied) Genome-wide association studies (GWAS) have been pivotal to increasing our understanding of intestinal disease. However, the mode by which genetic variation results in phenotypic change remains largely unknown, with many associated polymorphisms likely to modulate gene expression. Analyses of expression quantitative trait loci (eQTL) to date indicate that as many as 50% of these are tissue specific. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

199 Samples

Download data: CEL

(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) The majority of variants associated with complex traits and common diseases identified by genome-wide association studies (GWAS) map to noncoding regions of the genome with unknown regulatory effects. By leveraging ancestrally diverse biobank-scale GWAS data, massively parallel CRISPR screens and single cell transcriptomic and proteomic sequencing, we discovered target genes of noncoding variants for blood trait loci. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL18573 GPL24676

28 Samples

Download data: CSV, MTX, TSV, TXT

(Submitter supplied) Age-related macular degeneration (AMD) is a complex multifactorial disease with at least 34 loci contributing to genetic susceptibility. To gain functional understanding of AMD genetics, we generated transcriptional profiles of retina from 453 individuals including both controls and cases at distinct stages of AMD. We integrated retinal transcriptomes, covering 13,662 protein-coding and 1,462 noncoding genes, with genotypes at over 9 million common single nucleotide polymorphisms (SNPs) for expression quantitative trait loci (eQTL) analysis of a tissue not included in Genotype-Tissue Expression (GTEx) and other large datasets. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

523 Samples

Download data: TSV, TXT

(Submitter supplied) We conducted a genome-wide analysis to identify regulatory variants affecting the binding of NKX2-5, a core cardiac development transcription factor, and investigated their role in cardiac gene expression and EKG phenotypes. We generated iPSC-derived cardiomyocytes (iPSC-CMs) from a pedigree of seven whole-genome sequenced individuals, and profiled them with a variety of functional genomic assays including RNA-Seq, ATAC-Seq, and ChIP-Seq of both histone modification H3K27ac and NKX2-5. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis; Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL20301

32 Samples

Download data: BED, BW, TXT

(Submitter supplied) 30 B-lymphoblastoid cell lines (LCLs) with genome-wide genotype data were treated with hydrocortisone (GR agonist) and CORT108297 (GR modulator), followed by RNA-seq to identify PGx-eQTLs. We then integrated GR chromatin immunoprecipitation-sequencing (ChIP-seq) to characterize the epigenetic function of PGx-eQTLs that interfere with GR response elements. We also applied a high-throughput enhancer assay (STARR-seq) using PGx-eQTL loci DNA sequences to “scan” for drug-dependent SNPs.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

2 Samples

Download data: TBI, TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL24676 GPL20301

146 Samples

Download data: BED, TBI, TXT

(Submitter supplied) 30 B-lymphoblastoid cell lines (LCLs) with genome-wide genotype data were treated with hydrocortisone (GR agonist) and CORT108297 (GR modulator), followed by RNA-seq to identify PGx-eQTLs. We then integrated GR chromatin immunoprecipitation-sequencing (ChIP-seq) to characterize the epigenetic function of PGx-eQTLs that interfere with GR response elements. We also applied a high-throughput enhancer assay (STARR-seq) using PGx-eQTL loci DNA sequences to “scan” for drug-dependent SNPs.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

16 Samples

Download data: VCF

(Submitter supplied) 30 B-lymphoblastoid cell lines (LCLs) with genome-wide genotype data were treated with hydrocortisone (GR agonist) and CORT108297 (GR modulator), followed by RNA-seq to identify PGx-eQTLs. We then integrated GR chromatin immunoprecipitation-sequencing (ChIP-seq) to characterize the epigenetic function of PGx-eQTLs that interfere with GR response elements. We also applied a high-throughput enhancer assay (STARR-seq) using PGx-eQTL loci DNA sequences to “scan” for drug-dependent SNPs.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

8 Samples

Download data: BED, TXT