GEO DataSets

(Submitter supplied) We applied DNA content based flow cytometry methods to interrogate the genomes of clinical samples from 8 patients with ovarian cancer. These included 6 high grade serous ovarian carcinomas, a low grade serous carcinoma, and an endometriod carcinoma. Archived samples obtained from surgical resections from a University of California San Francisco (UCSF) tissue bank. Notably for this study we distinguished and sorted diploid and aneuploid tumors. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL9777

8 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Genome variation profiling by genome tiling array; Methylation profiling by array; Other

5 related Platforms

171 Samples

Download data: HIC, IDAT, NARROWPEAK, RDS, TXT

(Submitter supplied) CCCTC-binding factor (CTCF) regulates the 3D chromatin architecture by facilitating chromosomal loops. In addition to insulation of euchromatin from heterochromatin, CTCF is an important transcription factor and regulator of antigen receptor and T cell receptor recombination events. CTCF inactivating events have been found in human cancer, resulting in deregulation of global gene expression by altered methylated genomic states. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL2879 GPL9777 GPL4093

93 Samples

Download data: TXT

(Submitter supplied) Background: Patients with small intestinal neuroendocrine tumors (SINETs) frequently present with lymph node and liver metastases at the time of diagnosis, but the molecular changes that lead to the progression of these tumors are largely unknown. Sequencing studies have only identified recurrent point mutations in a single gene, CDKN1B, with heterozygous mutations in less than 10% of all tumors. Although SINETs are genetically stable tumors with a low frequency of point mutations and indels, they often harbor recurrent hemizygous copy number alterations (CNAs) yet the functional implications of these CNA are unclear. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

6 related Platforms

131 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Genome variation profiling by array; Other

Platforms:

GPL16791 GPL18573 GPL9777

7 Samples

Download data: HIC, TXT

(Submitter supplied) In this study, we compared the genomic landscape of resistant cell line HaCaT/SM to its progenitor HaCaT in order to gain insights into genetic changes associated with continuous alkylation and oxidative stress. We established chromosome numbers by cytogenetics, analyzed DNA copy number changes by means of array CGH, employed the genome-wide chromosome conformation capture technique Hi-C to detect chromosomal translocations and defined mutational signatures based on whole genome sequencing data. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL9777

3 Samples

Download data: TXT

(Submitter supplied) Three sample types are available: Primary patient samples after surgery that were flash-frozen and after short-term culture and after subsequent xenotransplantation into Nude rats or Nod/Scid, NSG or Nude mice. As well as longterm cell cultures derived from the xenotransplanted human tumors. Patient samples end with _B, mouse xenotransplanted tumors with_X and cell lines with_C. The preceeding numbers always indicate the patient association, whereas the following number inidcates mouse generation (X), passage number(C) or number of surgical samples (B) taken.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array; Genome variation profiling by array; Genome variation profiling by SNP array

5 related Platforms

69 Samples

Download data: TXT, XLSX

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by array

Platforms:

GPL16699 GPL9777

26 Samples

Download data: TXT

(Submitter supplied) To investigate the minimal genomic alterations in ameloblastoma, we have employed high-resolution CGH as a discovery platform to identify somatic genomic gains and losses in ameloblastoma tumors.

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL9777

8 Samples

Download data: TXT

(Submitter supplied) Copy number analysis to compare parental colorectal cancer cell lines and their selumetinib-resistant derivatives and identify gene copy changes that might contribute to resistance

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL9777

10 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL23382 GPL9777

78 Samples

Download data: TXT

(Submitter supplied) In this study we screened for changes of DNA methylation in response to X-irradiation in the lymphoblastoid cell line GM12878 and the primary lung fibroblast cell line IMR90. We employed methylated DNA-Immunoprecipitation in combination with genome wide and region specific DNA microarrays to identify preferences of radiation induced changes of methylation with respect to genomic and epigenomic characteristics.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL9777

12 Samples

Download data: TXT

(Submitter supplied) Clinical resection specimens of prostate tissue (radical prostatectomy and TUR-P) over the course of hormone deprivation therapy were flow sorted according to their DNA content (Ploidy) and subjected to aCGH analysis to identify possiple chromosomal abberations which could confer castration resistance.

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platforms:

GPL4091 GPL9777 GPL21857

28 Samples

Download data: TXT

(Submitter supplied) gDNA from patient samples with multiple basal cell carcinomas and possible exposure to ionizing radiation was hybridized Vs. GM12878 gDNA to assess CNAs. We aimed to find a possible common aberration pattern related to ionizing radiation or a rare metastasis.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL9777

6 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; Genome variation profiling by genome tiling array

15 related Platforms

30 Samples

Download data: CEL, IDAT, TXT

(Submitter supplied) Background: High-resolution microarray technology is routinely used in basic research and clinical practice to efficiently detect copy number variants (CNVs) across the entire human genome. A new generation of arrays combining high probe densities with optimized designs will comprise essential tools for genome analysis in the coming years. We systematically compared the genome-wide CNV detection power of all 17 available array designs from the Affymetrix, Agilent, and Illumina platforms by hybridizing the well-characterized genome of 1000 Genomes Project subject NA12878 to all arrays, and performing data analysis using both manufacturer-recommended and platform-independent software. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL9777

2 Samples

Download data: TXT

(Submitter supplied) The association between endometriosis, genomic copy number variant polymorphisms and differential gene expression is still unclear. The rationale of this study was to identify regions of copy number change in familial endometriosis, which could contain genes that may be involved with the susceptibility and progression of this disease.

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL9777

11 Samples

Download data: TXT

(Submitter supplied) Blinded study, melanoma tumor samples from patients treated with carboplatin and paclitaxel +/- sorafenib are compared aCGH of human melanoma tumor samples

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL9777

121 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing; Genome variation profiling by genome tiling array

Platforms:

GPL11154 GPL9115 GPL9777

27 Samples

Download data: TXT

(Submitter supplied) Next Generation Sequencing of Unmethylated Alu (NSUMA) interrogation of more than 130,000 individual Alus for differential methylation with concomitant analysis of copy number variations applied to the study of hypomethylation in colorectal cancer.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL9777

5 Samples

Download data: TXT