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Links from GEO DataSets

Items: 20

1.

Buccals are likely to be a more informative surrogate tissue than blood for epigenome-wide association studies [Illumina tiling]

(Submitter supplied) There is increasing evidence that interindividual epigenetic variation is an etiological factor in common human diseases. Such epigenetic variation could be genetic or non-genetic in origin, and epigenome-wide association studies (EWASs) are underway for a wide variety of diseases/phenotypes. However, performing an EWAS is associated with a range of issues not typically encountered in genome-wide association studies (GWASs), such as the tissue to be analyzed. more...
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL13534
22 Samples
Download data: TXT
Series
Accession:
GSE46573
ID:
200046573
2.

Buccals are likely to be a more informative surrogate tissue than blood for epigenome-wide association studies [Bisulfite-Seq]

(Submitter supplied) There is increasing evidence that interindividual epigenetic variation is an etiological factor in common human diseases. Such epigenetic variation could be genetic or non-genetic in origin, and epigenome-wide association studies (EWASs) are underway for a wide variety of diseases/phenotypes. However, performing an EWAS is associated with a range of issues not typically encountered in genome-wide association studies (GWASs), such as the tissue to be analyzed. more...
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL11154
28 Samples
Download data: TXT
Series
Accession:
GSE46572
ID:
200046572
3.

Buccals are likely to be a more informative surrogate tissue than blood for epigenome-wide association studies

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array; Methylation profiling by high throughput sequencing
Platform:
GPL13534
22 Samples
Download data
Series
Accession:
GSE45529
ID:
200045529
4.

Genome wide DNA methylation profiling of hyperplasias, primary endometrial cancer and metastases

(Submitter supplied) The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs in a total of 96 samples, including 8 hyperplasias, 33 endometrial cancers and 53 metastases, as well as 2 cell-lines.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL16304
96 Samples
Download data: IDAT
Series
Accession:
GSE67116
ID:
200067116
5.

Aging-associated DNA methylation changes in middle-aged individuals: The Young Finns Study

(Submitter supplied) Background Chronological aging-associated changes in the human DNA methylome are studied by multiple epigenome-wide association studies (EWAS); however, the aging-associated DNAmet changes identified among different age groups and tissues vary and especially the rates of aging-associated alterations in the epigenome during adulthood remain unclear. Here, we further explore and characterize CpG-sites where DNA methylation levels alter at a constant rate during adulthood and are also independent of blood cell type heterogeneity. more...
Organism:
Homo sapiens
Type:
Methylation profiling by array
Platform:
GPL13534
184 Samples
Download data: TXT
Series
Accession:
GSE69270
ID:
200069270
6.

A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies

(Submitter supplied) We developed a comprehensive analysis pipeline to conduct Epigenome-wide Association Studies (EWAS) using the Illumina Infinium HumanMethylation450 BeadChip, based on data from 2,664 individuals, and 36 samples measured in duplicate. We propose new approaches to quality control, data normalisation and batch correction through control-probe adjustment, and demonstrate that these improve data-quality. more...
Organism:
Homo sapiens
Type:
Methylation profiling by array
Platform:
GPL13534
2711 Samples
Download data: TXT
Series
Accession:
GSE55763
ID:
200055763
7.

Single-base resolution DNA methylation profiles of two highly inbred chicken lines, Leghorn and Fayoumi, by whole-genome bisulfite sequencing (MethylC-seq).

(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
Series
Accession:
GSE56975
ID:
200056975
8.

Methylation profiling in Ulcerative colitis

(Submitter supplied) The series was designed to identify the different methylated single CpGs involved in the pathophysiology of ulcerative colitis.
Organism:
Homo sapiens
Type:
Methylation profiling by array; Methylation profiling by genome tiling array
Platforms:
GPL8490 GPL13269
40 Samples
Download data: TXT
Series
Accession:
GSE27899
ID:
200027899
9.

Genome wide expression data from discordant twins (ulcerative colitis, primary mucosal tissue)

(Submitter supplied) Background and aims. The etiopathology of inflammatory bowel diseases is still poorly understood. To date, only few little data are available on the microbiota composition in ulcerative colitis (UC), representing a major subform of inflammatory bowel diseases. Currently, one of the main challenges is to unravel the interactions between genetics and environmental factors in the onset or during the progression and maintenance of the disease. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Dataset:
GDS4519
Platform:
GPL570
20 Samples
Download data: CEL
Series
Accession:
GSE22619
ID:
200022619
10.
Full record GDS4519

Monozygotic twin pairs discordant for ulcerative colitis: intestinal biopsies

Analysis of colon mucosal tissue from 10 monozygotic (MZ) twins discordant for ulcerative colitis (UC). Twins (paired samples) were analyzed to obtain mucosal response data independent of genetic variation. Results provide insight into molecular mechanisms underlying UC.
Organism:
Homo sapiens
Type:
Expression profiling by array, transformed count, 2 disease state, 10 individual sets
Platform:
GPL570
Series:
GSE22619
20 Samples
Download data: CEL
11.

Genome-wide DNA methylation profiling in the superior temporal gyrus reveals epigenetic signatures associated with Alzheimer's disease

(Submitter supplied) Recent work has identified roles for environmental, genetic and epigenetic factors in AD risk. Motivated by suspected roles for epigenetic modifications in AD, we performed a genome-wide screen of DNA methylation using the Illumina Infinium HumanMethylation450 array platform on bulk tissue samples from the superior temporal gyrus (STG) of AD cases and non-demented controls. We paired a sliding window approach with linear models that account for age, gender, ethnicity, and estimated cellular proportions (neuronal vs. more...
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL13534
68 Samples
Download data: TXT
Series
Accession:
GSE76105
ID:
200076105
12.

Peripheral Blood Methylation Profiling of Female Crohn’s Disease Patients

(Submitter supplied) Genome wide DNA methylation profiling of female Crohn's disease patients versus healthy female controls. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 485,000 CpGs in peripheral blood samples. Samples included 25 healthy controls and 18 female patients with histologically confirmed CD.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL16304
40 Samples
Download data: IDAT
Series
Accession:
GSE81961
ID:
200081961
13.

ChIP-chip from the follicular lymphoma cell line RL with H3K4me3, H3K37me3 and Suz12

(Submitter supplied) We conducted genome-wide bisulfite sequencing analysis of the follicular lymphoma cell line RL and found that a large amount of methylated genes are polycomb target genes in ES cells. We therefore conducted a ChIP-chip experiment to determine the methylated genes that are bound by the polycomb protein Suz12. Although 28% of MRIs are PRC2 target genes in ES cells, our ChIP-on-Chip analysis showed that only 13% of MRIs are associated with H3K27Me3 marks and only 5% of the MRIs are bound by Suz12 in RL cells in vivo.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL7408
3 Samples
Download data: PAIR
Series
Accession:
GSE20019
ID:
200020019
14.

Genome-Wide Analysis of Acute Myeloid Leukemia Reveals Leukemia-Specific Methylome and Subtype-Specific Hypomethylation of Repeats

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing; Expression profiling by array
Platforms:
GPL9115 GPL9851
22 Samples
Download data: GFF, WIG
Series
Accession:
GSE37022
ID:
200037022
15.

Gene expression profiling of Acute Myeloid Leukemia (AML) samples

(Submitter supplied) The aim was to analyze the expression of genes in cytogenetically distinct cases of AML.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL9851
6 Samples
Download data
Series
Accession:
GSE34722
ID:
200034722
16.

Genome-wide study of DNA methylation in AML by MeDIP-seq

(Submitter supplied) Methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq) has the potential to identify changes in DNA methylation important in cancer development. In order to understand the role of epigenetic modulation in the development of acute myeloid leukemia (AML) we have applied MeDIP-seq to the DNA of 12 AML patients and 4 normal bone marrows. This analysis revealed leukemia-associated differentially methylated regions that included gene promoters, gene bodies, CpG islands and CpG island shores. more...
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL9115
16 Samples
Download data: GFF, TXT, WIG
Series
Accession:
GSE28314
ID:
200028314
17.

DNA methylation in peripheral blood from individuals with Crohns' disease or ulcerative colitis and normal controls

(Submitter supplied) Genome wide DNA methylation profiling of Crohn's disease, ulcerative colitis, and normal peripheral blood samples. The Illumina Infinium HumanMethylation450 BeadChip v1.1 was used to obtain DNA methylation profiles across 482,421 CpGs in peripheral blood samples. Samples came from 17 Crohn's disease affected, 11 ulcerative colitis affected, and 20 normal individuals. Within these samples were three twin sets discordant for Crohn's disease and three twin sets discordant for ulcerative colitis.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL13534
48 Samples
Download data: TXT
Series
Accession:
GSE32148
ID:
200032148
18.

Epigenome analysis of tumor adjacent normal tissue from breast cancer patients

(Submitter supplied) Genome wide DNA methylation profiling of tumor adjacent normal tissue from patients with invasive breast cancer, as well as tissue from women undergoing reduction mammoplasty or prophylactic surgery. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 485,577 CpGs in snap frozen breast tissue. Samples included 70 tumor-adjacent normal breast tissue with invasive disease, 8 tissues from breast prophylactic patients, and 18 tissues from breast reduction patients.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL13534
96 Samples
Download data: TXT
Series
Accession:
GSE67919
ID:
200067919
19.

Epigenome profiling reveals significant DNA demethylation of interferon signature genes in lupus neutrophils

(Submitter supplied) We identified genome-wide DNA methylation patterns within neutrophils and low-density granulocytes of Lupus patients and demographically matched controls
Organism:
Homo sapiens
Type:
Methylation profiling by array
Platform:
GPL13534
38 Samples
Download data: TXT
Series
Accession:
GSE65097
ID:
200065097
20.

Comparison of DNA methylation in human tissues

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL9115 GPL11154
9 Samples
Download data: BED, TAR
Series
Accession:
GSE39777
ID:
200039777
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