GEO DataSets

(Submitter supplied) Arsenic is methylated during its metabolism, thereby depleting the intracellular methyl donor S-adenosyl-methionine, which may lead to disturbances in DNA methylation patterns which could lead to altered gene expression

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16356

24 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL16356 GPL16284

48 Samples

Download data: CEL, PAIR

(Submitter supplied) Arsenic is methylated during its metabolism, thereby depleting the intracellular methyl donor S-adenosyl-methionine, which may lead to disturbances in DNA methylation patterns

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL16284

24 Samples

Download data: PAIR

(Submitter supplied) Genome wide DNA methylation profiling of normal and adenocarcinoma lung tissues. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in lung adenocarcinoma samples.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

88 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL13534 GPL10558

253 Samples

Download data

(Submitter supplied) Lung cancer is the worldwide leading cause of death from cancer. DNA methylation in gene promoter regions is a major mechanism of gene expression regulation that may promote tumorigenesis. Experimental Design Whole-genome DNA methylation analysis using 450K Illumina BeadArrays was performed on 12 normal lung tissues and 124 tumors including 83 adenocarcinomas, 23 squamous cell carcinomas (SqCC), one adenosquamous cancer, five large cell carcinomas, nine large cell neuroendocrine carcinomas (LCNEC), and three small cell carcinomas (SCLC). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

117 Samples

Download data: TXT

(Submitter supplied) Lung cancer is the worldwide leading cause of death from cancer. DNA methylation in gene promoter regions is a major mechanism of gene expression regulation that may promote tumorigenesis. However, whether clinically relevant subgroups based on DNA methylation patterns exist in lung cancer is not well studied. We performed whole-genome methylation analysis using 450K Illumina BeadArrays on 124 tumors including 83 adenocarcinomas, 23 squamous cell carcinomas, one adenosquamous cancer, five large cell carcinomas, nine large cell neuroendocrine carcinomas (LCNEC), three small cell carcinomas (SCLC) and 12 normal lung tissues. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

136 Samples

Download data: TXT, XLS

(Submitter supplied) Arsenic (As) exposure is a significant worldwide environmental health concern. Low dose, chronic arsenic exposure has been associated with higher risk of skin, lung, and bladder cancer, as well as cardiovascular disease and diabetes. While arsenic-induced biological changes play a role in disease pathology, little is known about the dynamic cellular changes due to arsenic exposure and withdrawal. In these studies, we seek to understand the molecular mechanisms behind the biological changes induced by chronic low doses of arsenic exposure. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

8 Samples

Download data: CEL

(Submitter supplied) Inorganic arsenic, a ubiquitous environmental contaminant of food and drinking water, is a human carcinogen associated with lung, liver, prostate, renal, and bladder cancers. It has been postulated that inorganic arsenic targets stem cells or partially differentiated progenitor cells, causing their oncogenic transformation. This is proposed to be one of the key mechanisms in arsenic-associated carcinogenesis; however, the underlying mechanisms for this process remain largely unknown. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL16699 GPL20844

14 Samples

Download data: TXT

(Submitter supplied) Methods: The cDNA libraries from 3 pooled samples of cultured cells for each group were sequenced to generate RNA profiles using Illumina Miseq platform Results: The sequencing runs yielded a total of 95.01 M reads with an average length of 73-74 bp. The high-throughput sequencing performed for liver samples with different treatments showed similar numbers of yielded reads ranged from 5.57 to 5.74 M and the same average length. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15520

4 Samples

Download data: TXT

(Submitter supplied) We demonstrate that expression of key markers of keratinocyte differentiation is suppressed by exposure to sodium arsenite. Folate deficiency exacerbates this effect. In addition, cancer-related cell movement genes, and growth and proliferation genes are altered. Several redox-sensitive transcription factors are implicated in mediating these gene expression changes due to arsenic treatment and folate deficiency. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS2872

Platform:

GPL1261

24 Samples

Download data: CEL

Analysis of skin from transgenic K6/ODC animals maintained on a folate deficient diet and exposed to 1 or 10 ppm sodium arsenate. K6/ODC mice develop skin tumors when exposed to sodium arsenite. Results provide insight into the combined effect of folate deficiency and arsenic on the skin.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 agent, 3 dose, 2 protocol sets

Platform:

GPL1261

Series:

GSE8733

24 Samples

Download data: CEL

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

Organism:

Homo sapiens; synthetic construct

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL19117 GPL15207

36 Samples

Download data: CEL

(Submitter supplied) Determining the miRNA and mRNA expression profiles in HaCaT cells at early and late stages of arsenite exposure to reveal early and late changes in the HaCaT cells transformation process.

Organism:

Homo sapiens; synthetic construct

Type:

Non-coding RNA profiling by array

Platform:

GPL19117

18 Samples

Download data: CEL

(Submitter supplied) Determining the miRNA and mRNA expression profiles in HaCaT cells at early and late stages of arsenite exposure to reveal early and late changes in the HaCaT cells transformation process.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

18 Samples

Download data: CEL

(Submitter supplied) Epigenetic changes through altered DNA methylation have been implicated with critical aspects of tumor progression, and have been extensively studied in cancer cells and tumor tissue samples. In contrast, our current knowledge of the aberrant genomic methylation in tumor-associated fibroblasts (TAFs), which are critical co-conspirators of tumor progression, is very scarce. To address this gap of knowledge, we conducted genome-wide DNA methylation profiling on lung TAFs and paired control fibroblasts (CFs) from surgical non-small cell lung cancer patients. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

28 Samples

Download data: TXT

(Submitter supplied) Arsenic is a carcinogen that is known to induce cell transformation and tumor formation. Although studies have been performed to examine the modulation of signaling molecules caused by arsenic exposure, the molecular mechanisms by which arsenic causes cancer are still unclear. We hypothesized that arsenic alters gene expression leading to carcinogenesis in the lung. In this study, we examined global gene expression in response to 0.75 µM arsenic treatment for 1-7 days in a rat lung epithelial cell line (L2) using an in-house 10k rat DNA microarray. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL5484

30 Samples

Download data

(Submitter supplied) The present study used microarray expression profiling to determine the effects of embryonic arsenic exposure. Fertilized killifish (Fundulus heteroclitus) eggs were exposed to 0, 5, 15, or 25ppm arsenic as sodium arsenite. To examine differentially expressed genes, the microarrays were probed using RNA obtained from the control and 25ppm-exposed killifish just after hatching. No differences were noted in survival or hatching success between any of the groups. more...

Organism:

Fundulus heteroclitus

Type:

Expression profiling by array

Platform:

GPL13723

20 Samples

Download data: TXT

(Submitter supplied) Both epidemiological investigations and animal studies have linked arsenic-contaminated water to cancers, in- cluding skin, liver and lung cancers. Besides genotoxicity, arsenic exposure-related pathogenesis of disease is widely considered through epigenetic mechanisms; however, the underlying mechanism remains to be deter- mined. Herein we explore the initial epigenetic changes via acute sodium arsenite (As) exposures of mouse em- bryonic fibroblast (MEF) cells and histone H3K79 methyltransferase Dot1L knockout (Dot1L−⁠ /−) MEF cells. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL21273

6 Samples

Download data: BW, TXT

(Submitter supplied) Ground water Arsenic (As) toxicity is a global problem and millions of people are exposed to elevated levels (more than WHO advised maximum limit of 10µg/L) through drinking water. The exposure is associated with various cancerous and non-cancerous diseases. It may alter DNA methylation profiles of inviduals and suppress the activity of various genes giving rise to different diseases. Pakistan, a developing country in South Asian region, also has reported elevated ground water As levels in various investigations since 2005. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL16284

57 Samples

Download data: PAIR, TXT