GEO DataSets

Analysis of leukocytes from regionally distinct groups of Moroccan Amazighs leading diverse lifestyles: nomadic, rural, and urban. The Amazighs represent a genetically relatively homogeneous population. Results provide insight into effect of environment on immune function and disease susceptibility.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 gender, 3 individual sets

Platform:

GPL5764

Series:

GSE8847

46 Samples

Download data: TXT

(Submitter supplied) The human transitions from nomadic to agrarian to urban lifestyles are likely to impact physiology and disease susceptibility. In order to estimate the magnitude of the impact of lifestyle on genome function, we profiled gene expression in total leukocytes of Moroccan Amazigh from three distinct localities. Despite great expression heterogeneity in humans, as much as one third of the PBMC transcriptome was found to differ between the localities. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4283

Platform:

GPL5764

46 Samples

Download data: TXT

(Submitter supplied) Genome-wide association studies of transcript abundance in peripheral blood samples or derivative cell lines have demonstrated a preponderance of eSNP effects that, for the most part, involve regulatory polymorphisms in the differentially expressed gene. Several of these highlight associations that contribute to a variety of disease conditions, but the question arises as to how the associations are affected by the environment. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

194 Samples

Download data: TXT

(Submitter supplied) To better characterize smoking–associated methylation changes in whole blood, we used Illumina HumanMethylation450 BeadChip to assess DNA samples from current (SM, n=172) and never smokers (NS, n=81).

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

253 Samples

Download data: IDAT, TXT

(Submitter supplied) Using neutrophils from a cohort of normal individuals, we generated transcriptomic profile of 4 individuals.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: XLSX

(Submitter supplied) Using neutrophils from a cohort of normal individuals, we generated base-resolution DNA methylation maps to document inter-individual epigenetic variation.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

13 Samples

Download data: TXT, XLSX

(Submitter supplied) The goal of the experiment – genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters Keywords: DNA methylation, Methylated CpG island amplification coupled with promoter arrays, normal tissue

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

4 related Platforms

4 Samples

Download data

(Submitter supplied) Here we provided the first single-base resolution DNA methylatome in chicken lungs by whole-genome bisulfite sequencing (MethylC-seq). In addition, two genetically distinct highly inbred chicken lines, Leghorn and Fayoumi, were used to examine how DNA methylation regulates mRNA gene expression between two lines. The methylation profile demonstrated that methylcytosines in the chicken were more likely to occur in CG dinucleotides than in non-CG sites. more...

Organism:

Gallus gallus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9385

2 Samples

Download data: TXT

(Submitter supplied) B-cell precursor acute lymphoblastic leukemia (pre-B ALL) is the most common pediatric cancer. Although the genetic origin of the disease remains unclear, epigenetic modifications including DNA methylation are suggested to contribute significantly to leukemogenesis. We assessed the DNA methylation status of 402,842 CpG-sites across the genome (Illumina 450k array) in tumor and remission samples of 46 pre-B ALL patients, thus generating the most comprehensive single CpG-site resolution pre-B ALL methylomes so far. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

92 Samples

Download data: TXT

(Submitter supplied) The pathophysiology of intervertebral disc (IVD) degeneration is not entirely understood; however, environmental and endogenous factors under genetic predisposition are considered to initiate the degenerative changes of human IVDs. Aberrant epigenetic alterations play a pivotal role in several diseases, including osteoarthritis. However, epigenetic alternations, including DNA methylation, in IVD degeneration have not been evaluated. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

16 Samples

Download data: IDAT, TXT

(Submitter supplied) DNA methylation is an important epigenetic modification involved in many biological processes and diseases. Many studies have mapped DNA methylation changes associated with embryogenesis, cell differentiation and cancer at a genome-wide scale. Our understanding of genome-wide DNA methylation changes in a developmental or disease-related context has been steadily growing. However, the investigation of which CpGs are variably methylated in different normal cell or tissue types is still limited. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing; Third-party reanalysis

Platforms:

GPL9115 GPL11154

31 Samples

Download data: TXT

(Submitter supplied) DNA methylation analysis of DNA samples from total WBC collection The DNA samples from each subject was first subject to bisulfite conversion, followed by sample preparation and microarray experiment.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

36 Samples

Download data: IDAT

(Submitter supplied) Transcriptome analysis of pooled RNA samples from total WBC collection The RNA samples from six subjects were evenly pooled into one pooled one, followed by sample preparation and microarray experiment.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

9 Samples

Download data: CEL, CHP

(Submitter supplied) The most common congenital heart disease (CHD) is the ventricular septal defect (VSD), which is also a subfeature of Tetralogy of Fallot (TOF) representing the most common form of cyanotic CHD. The underlying causes for the majority of CHDs are still unclear and most probably consist of combinations of genetic, epigenetic and environmental factors. DNA methylation is the most widely studied epigenetic modification and several cardiac regulators have already been shown to be differentially methylated in CHD patients. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

23 Samples

Download data: TXT

(Submitter supplied) Right ventricular mRNA profiles from 22 patients with Tetralogy of Fallot (TOF) and mRNA-seq profiles from the left and right ventricle (LV and RV, respectively) of 4 healthy unaffected individuals (NH) were generated. The total RNA was isolated from the 30 human heart samples using TRIzol. mRNAs were isolated from total RNA and prepared for sequencing using Illumina Kit RS-100-0801 according to the manufacturer's protocol (Preparing Samples for Sequencing of mRNA Sept 2008). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9052

30 Samples

Download data: TXT

(Submitter supplied) Confounding due to cellular heterogeneity represents one of the foremost challenges currently facing Epigenome-Wide Association Studies (EWAS). Statistical methods leveraging the tissue-specificity of DNA methylation for deconvoluting the cellular mixture of heterogeneous biospecimens such as whole blood, offer a promising solution. However, their performance depends entirely on the library of DNA methylation markers being used as the basis for deconvolution. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

18 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) Whole peripheral blood samples collected into Tempus tubes from 189 adult participants in the Center for Health Discovery and Well Being study of Emory University and Georgia Tech, in Midtown Atlanta. The sample is of mixed ethnicity, and is part of a survey of the impact of genetics and lifestyle on gene expression and clinical attributes. Sample annotations include gender, self-reported ethnicity, zipcode of current address, and percent body fat, as well as technical features of the study (Sentrix plate ID, date of hybridization, and RNA quality RIN score.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

189 Samples

Download data: TXT

(Submitter supplied) This study explores the impact of lifestyle and environment on gene expression through whole transcriptome profiling of peripheral blood samples in Fijian population (native Melanesians and Indians) living in the rural and urban areas.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

41 Samples

Download data: TXT