GEO DataSets

(Submitter supplied) African Americans (AAs) are disproportionately affected by metabolic diseases and adverse drug events, with limited publicly available genomic and transcriptomic data to advance the knowledge of the molecular underpinnings or genetic associations to these diseases or drug response phenotypes. To fill this gap, we obtained 60 primary hepatocyte cultures from AA liver donors for genome-wide mapping of expression quantitative trait loci (eQTL) using LAMatrix. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL24127

96 Samples

Download data: IDAT, TXT

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

Organism:

Homo sapiens

Type:

Methylation profiling by array; Expression profiling by high throughput sequencing; Genome variation profiling by SNP array

4 related Platforms

567 Samples

Download data: IDAT, TXT

(Submitter supplied) In African Americans (AA), the proportion of West African ancestry (WAA) may explain the genetic drivers of health disparities in disease. Analysis of RNA sequencing data from sixty AA-derived primary hepatocytes identified 32 gene expression profiles associated with WAA (FDR <0.05) with enrichment in angiogenesis and inflammatory pathways (FDR <0.1). Association of DNA methylation to WAA identified 1037 differentially methylated regions (FDR <0.05), with hypomethylated genes enriched for drug response pathways. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL16791

60 Samples

Download data: TXT

(Submitter supplied) In African Americans (AA), the proportion of West African ancestry (WAA) may explain the genetic drivers of health disparities in disease. Analysis of RNA sequencing data from sixty AA-derived primary hepatocytes identified 32 gene expression profiles associated with WAA (FDR <0.05) with enrichment in angiogenesis and inflammatory pathways (FDR <0.1). Association of DNA methylation to WAA identified 1037 differentially methylated regions (FDR <0.05), with hypomethylated genes enriched for drug response pathways. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL23976

56 Samples

Download data: IDAT, XLSX

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

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array; Expression profiling by high throughput sequencing

Platforms:

GPL21145 GPL16791

58 Samples

Download data: IDAT

(Submitter supplied) Systemic sclerosis is a multisystem autoimmune disorder that has an unclear etiology and disproportionately affects African Americans (AA). Additionally, monocytes show heightened activation in SSc, and in AA relative to European ancestry (EA) individuals. Monocytes are thus a good target tissue for elucidating disease mechanisms. In this study, we sought to identify differentially expressed genes in classical monocytes from AA SSc patients relative to unaffected AA controls. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

34 Samples

Download data: TXT

(Submitter supplied) Systemic sclerosis is a multisystem autoimmune disorder that has an unclear etiology and disproportionately affects African Americans (AA). Additionally, monocytes show heightened activation in SSc, and in AA relative to European ancestry (EA) individuals. Monocytes are thus a good target tissue for elucidating disease mechanisms. In this study, we sought to investigate differentially methylated loci in classical monocytes from AA SSc patients and unaffected AA controls. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

24 Samples

Download data: IDAT, TXT

(Submitter supplied) Genome wide DNA methylation profiling of normal and adjacent OSCC samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 4,50,000 CpGs in tissue samples. Total 21 samples were taken including 10 paired and 1 unpaired tissues. 6 were HPV Positive and 5 were HPV negative.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

21 Samples

Download data: IDAT

(Submitter supplied) Background. The etiology and reasons underlying the ethnic disparities in systemic sclerosis (SSc) remain unknown. African-Americans (AA) are disproportionally affected by SSc, yet dramatically underrepresented in research. The role of DNA methylation in disease risk remains unclear. This analysis was conducted to comprehensive identify differentially methylated loci associated with SSc in AA. Methods. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

30 Samples

Download data: COV

(Submitter supplied) Background: African Americans (AA) have increased burdens of cardiovascular disease and cancer compared to Caucasian Americans (CA). This study addresses the possibility that genetic differences affecting the biology of the vascular endothelium could be a factor contributing to this health disparity. Methods: From self-identified, healthy, 20-29 year old AA (n=21) and CA (n=17), we established cultures of blood outgrowth endothelial cells (BOEC) and applied microarray profiling. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

38 Samples

Download data: CEL

(Submitter supplied) Genome wide Methylation profiling of DNA extracted from plaques of atherosclerotic plaque samples (n=14) and of controls (n=4). The Illumina Infinium HumanMethylation450 or HumanMethylation850 BeadChip was used representing potentially methylated CpG sites throughout the genome.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL16304 GPL23976

18 Samples

Download data: IDAT

(Submitter supplied) Women of sub-Saharan African descent have disproportionately higher incidence of Triple Negative Breast Cancer (TNBC), and TNBC-specific mortality. Population comparative studies show racial differences in TNBC biology, including higher prevalence of basal-like and Quadruple-Negative subtypes in African Americans (AA). However, previous investigations relied on self-reported race (SRR) of primarily United States (US) populations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

26 Samples

Download data: TXT

(Submitter supplied) A microarray targeting promoters of cancer-related genes was used to evaluate DNA methylation at 935 CpG sites in 517 invasive breast tumors from the Carolina Breast Cancer Study (CBCS), a population-based study of invasive breast cancer. Concensus clustering using methylation (β) values for the 167 most variant CpG loci defined 4 clusters differing most distinctly in hormone receptor (HR) status, intrinsic subtype (luminal versus basal-like) and p53 mutation status. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

526 Samples

Download data: TXT

(Submitter supplied) Background: Genetic and epigenetic variability contributes to the susceptibility and pathogenesis of autoimmune diseases. T cells play an important role in several autoimmune conditions, including lupus, which is more common and more severe in people of African descent. To investigate inherent epigenetic differences in T cells between ethnicities, we characterized genome-wide DNA methylation patterns in naïve CD4+ T cells in healthy African-Americans and European-Americans, and then confirmed our findings in lupus patients. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL13534

66 Samples

Download data: TXT

(Submitter supplied) Epigenome-wide profiling of placental DNAm in samples obtained from 72 smokers enrolled in the VCSIP RCT: NCT03203603 (35 supplemented with placebo, 37 supplemented with vitamin C) and 24 never-smokers for reference.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

96 Samples

Download data: IDAT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Platforms:

GPL13534 GPL14550

141 Samples

Download data: IDAT, TXT

(Submitter supplied) We compared genomic DNA methylation patterns and gene expression in African American children with persistent atopic asthma versus healthy controls. We identified 119 differentially methylated regions (DMRs) and 118 differentially methylated probes (DMPs) after adjustment for age, gender, race/ethnicity, batch effects, inflation, and multiple comparisons (false discovery rate-adjusted q<0.05). Genes differentially methylated include those with established roles in asthma and atopy, components of the extracellular matrix, genes related to immunity, cell adhesion, epigenetic regulation, and airway obstruction. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14550

69 Samples

Download data: TXT

(Submitter supplied) Background: Nasal epithelia are emerging as a proxy measure of gene expression of the airway epithelium in asthma. We hypothesized that epigenetic marks regulate gene expression of the nasal epithelia and consequently may provide a novel target for allergic asthma. Methods: We compared genomic DNA methylation patterns and gene expression in African American children with persistent atopic asthma [N=36] versus healthy controls [N=36]. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

72 Samples

Download data: IDAT

(Submitter supplied) Genome-wide DNA methylation profiling of normal and tumor tissue samples of 7 pancreatic ductal adenocarcinoma patients.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

14 Samples

Download data: IDAT, TXT

(Submitter supplied) Multiple joint data, including methylome, transcriptomic, BRAF V600E mutation results and clinical features, aiming to identify molecular drivers in papillary thyroid carcinomas.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

82 Samples

Download data: IDAT