GEO DataSets

(Submitter supplied) Radiation therapy is used to treat half of all cancer patients. Response to radiation therapy varies widely among patients. Therefore, we performed a genome-wide association study (GWAS) to identify biomarkers to help predict radiation response using 277 ethnically defined human lymphoblastoid cell lines (LCLs). Basal gene expression levels (Affymetrix) and 1.3 million genome-wide SNP markers (Illumina) were assayed for all 277 human LCLs. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL6988

288 Samples

Download data: CSV

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

Organism:

Homo sapiens

Type:

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

4 related Platforms

862 Samples

Download data: CEL

(Submitter supplied) Radiation therapy is used to treat half of all cancer patients. Response to radiation therapy varies widely among patients. Therefore, we performed a genome-wide association study (GWAS) to identify biomarkers to help predict radiation response using 277 ethnically defined human lymphoblastoid cell lines (LCLs). Basal gene expression levels (Affymetrix) and 1.3 million genome-wide SNP markers (Illumina) were assayed for all 277 human LCLs. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL6987

95 Samples

Download data: CSV

(Submitter supplied) Radiation therapy is used to treat half of all cancer patients. Response to radiation therapy varies widely among patients. Therefore, we performed a genome-wide association study (GWAS) to identify biomarkers to help predict radiation response using 277 ethnically defined human lymphoblastoid cell lines (LCLs). Basal gene expression levels (Affymetrix) and 1.3 million genome-wide SNP markers (Illumina) were assayed for all 277 human LCLs. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL6434

192 Samples

Download data: CSV

(Submitter supplied) We used microarrays to identify the variation of basal gene expression level among 287 lymphoblastoid cell lines. Radiation therapy is used to treat half of all cancer patients. Response to radiation therapy varies widely among patients. Therefore, we performed a genome-wide association study (GWAS) to identify biomarkers to help predict radiation response using 277 ethnically defined human lymphoblastoid cell lines (LCLs). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

287 Samples

Download data: CEL

(Submitter supplied) We used microarrays to identify the expression differences of FKBP5 gene between the pancreatic tumor and normal samples.On average normal samples had more FKBP5 expression compared to tumor samples

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4102

Platform:

GPL570

52 Samples

Download data: CEL

Analysis of tumor tissue and normal tissue in pancreatic cancer samples. The fresh frozen samples were obtained during surgical procedures. Results provide insight into molecular mechanisms underlying tumorigenesis.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 tissue sets

Platform:

GPL570

Series:

GSE16515

52 Samples

Download data: CEL

(Submitter supplied) Gene expression profiling of pancreatic cancer cell CFPAC-1 when BACH1 knockdown. BACH1 is a transcription repressor and its regulation networks is poorly understood in pancreatic ductal adenocarcinoma. We used the total RNA from shControl and shBACH1 CFPAC-1 cells to analyze the differentially expressed genes which were regulated by BACH1, and further explored the biological processes that BACH1 may involved.

Organism:

Homo sapiens

Type:

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

Platform:

GPL19615

1 Sample

Download data: TXT

(Submitter supplied) We measured the methylation status at 27,578 CpG sites using the Human Methylation27 DNA array in 77 HapMap Yoruba lymphoblastoid cell lines.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

160 Samples

Download data: IDAT, TXT

(Submitter supplied) Purpose: We examined the extent and nature of non-genetic variability at the gene regulatory activity and gene expression levels in isogenic LCLs, highlighting features of the LCL model that might aid the rational design of genetic association studies. Brief method: H3K27ac ChIP-Seq: Crosslinked chromatin corresponding to 5 million cells was immunoprecipitated with 2.5 ug anti-histone H3 (acetyl K27) antibody (Abcam, cat. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL18573

26 Samples

Download data: TXT

(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) DNA methylation (5-mC) and hydroxymethylation (5-hmC) are regarded as important epigenetic hallmarks in the carcinogenesis of colorectal cancer by transcriptional regulation. 5hmC is an intermediate during active demethylation and maintains the equilibrium of DNA methylation. Previous studies on DNA methylation don’t differentiate 5-hmC from 5-mC. Here, in order to elucidate the epigenetic mechanisms of carcinogenesis of colorectal cancer, we integrate genome wide levels of 5-mC, 5-hmC and Transcriptional expression. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL11154

36 Samples

Download data: TXT, WIG, XML

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL11154

102 Samples

Download data

(Submitter supplied) Noncoding transcription is a defining feature of active enhancers, linking transcription factor (TF) binding to the molecular mechanisms controlling gene expression. To determine the relationship between enhancer activity and biological outcomes in breast cancers, we profiled the transcriptomes (using GRO-seq and RNA-seq) and epigenomes (using ChIP-seq) of 13 different breast cancer cell lines representing the five major molecular subtypes of breast cancer. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

52 Samples

Download data: BW

(Submitter supplied) Noncoding transcription is a defining feature of active enhancers, linking transcription factor (TF) binding to the molecular mechanisms controlling gene expression. To determine the relationship between enhancer activity and biological outcomes in breast cancers, we profiled the transcriptomes (using GRO-seq and RNA-seq) and epigenomes (using ChIP-seq) of 13 different breast cancer cell lines representing the five major molecular subtypes of breast cancer. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

50 Samples

Download data: BW

(Submitter supplied) Chromatin architecture is essential to transcriptional regulation. Cancer cells undergo critical chromatin remodeling processes that interact with the activation or silencing of oncogenes or tumor suppressor genes. These processes, together with other alterations of the functional status of chromatins, are characterized by epigenetic marks such as covalent histone modifications, DNA methylations and etc. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

273 Samples

Download data: WIG

(Submitter supplied) The common genetic variants associated with complex traits typically lie in non-coding DNA and may alter gene regulation in a cell-type specific manner. Consequently, the choice of tissue or cell model in the dissection of disease associations is important. We carried out an eQTL study of primary human osteoblasts (HOb) derived from unrelated donors of Swedish origin, each represented by two independently derived primary lines to provide biological replication. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6104

187 Samples

Download data: TXT

(Submitter supplied) To define methylation markers of breast cancer for circulating tumor DNA, we compare the methylation characteristics of breast cancer and blood DNA of healthy individuals.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

119 Samples

Download data: TXT

(Submitter supplied) Using a functional approach to investigate the epigenetics of Type 2 Diabetes (T2D), we combine three lines of evidence – diet-induced epigenetic dysregulation in mouse, epigenetic conservation in humans, and T2D clinical risk evidence – to identify genes implicated in T2D pathogenesis through epigenetic mechanisms related to obesity. Beginning with dietary manipulation of genetically homogeneous mice, we identify differentially DNA-methylated genomic regions. more...

Organism:

Homo sapiens; Mus musculus

Type:

Methylation profiling by genome tiling array

Platforms:

GPL19521 GPL19520

86 Samples

Download data: TXT, XYS

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL20301

54 Samples

Download data: BED