GEO DataSets

(Submitter supplied) Gene expression profiling of RNA and SNP array profiling of DNA was performed on Burkitt lymphoma samples to identify genes and pathways affected by DNA copy number alterations and expression changes.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL3718 GPL570

112 Samples

Download data: CEL

(Submitter supplied) To identify genetic alterations involved in the pathogenesis of PETs, we have analysed a total of 32 PET samples (29 tissue specimens and 3 cell lines) using high-resolution single nucleotide polymorphism (SNP) arrays. Keywords: comparative genomic hybridisation

Organism:

Homo sapiens

Type:

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

Platforms:

GPL3718 GPL3720

104 Samples

Download data: CEL, CHP

(Submitter supplied) Esophageal squamous cell carcinoma (ESCC) is an aggressive cancer with one of the highest world incidences in the Eastern Cape region of South Africa. Several genome wide studies have been performed on ESCC cohorts from Asian countries, North America, Malawi and other parts of the world but none has been conducted on ESCC tumors from South Africa to date, where the molecular pathology and etiology of this disease remains unclear. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL3718 GPL3720

162 Samples

Download data: CEL, TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL3720 GPL6804 GPL3718

152 Samples

Download data: CEL

(Submitter supplied) Since ESCC is a complex and heterogeneous disease, it is increasingly important that analyses combine the evaluation of alterations in DNA, including somatic copy number alterations (SCNA), which distinguished from germ line copy number variants, allelic imbalance and LOH, and RNA, including those that occur in both mRNA and miRNA on the same specimen. Thus, in order to better understand their potential interactions in the development of cancers, in the present study, we studied alterations at DNA level as well as expression of mRNA and target miRNA in tumors and their matched normal tissues from 56 ESCC cases on a candidate tumor suppressor gene CSMD1 to characterize there alterations in this gene for import insights into the cellular detect that cause the complex disease, ESCC.

Organism:

Homo sapiens

Type:

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

Platforms:

GPL3718 GPL3720

80 Samples

Download data: CEL

(Submitter supplied) When characterizing novel cell lines, we used SNP genotyping alignment to compare the tumor to the resulting cell line. In order to do this pairwise comparison as each cell model was developed, we added additional data from the GEO database during the normalization step. These data were either tumor DNA or cancer cell line DNA. These samples were not part of a matched pair and so genotype alignment was not reported for these samples. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array; Third-party reanalysis

Platform:

GPL3718

15 Samples

Download data: CEL, TXT

(Submitter supplied) To identify chromosomal alterations in ATL, SNP array analyses were performed in 19 leukemia cell samples from ATL patients and 9 ATL-related cell lines. ATL displayed complex chromosomal abnormalities, but it contained recurrent chromosomal amplification and deletion, including 14q11 and 14q32, which may be associated with the development of ATL. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved peripheral blood samples and from cell line samples.

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array

Platforms:

GPL3720 GPL3718

28 Samples

Download data: CEL, CHP

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. A valuable approach to understand how individual and population genetic differences can predispose to disease is to assess the impact of genetic variants on cellular functions (e.g., gene expression) of cell and tissue types related to pathological states. To understand the genetic basis of nonsyndromic cleft lip with or without cleft palate (NSCL/P) susceptibility, a complex and highly prevalent congenital malformation, we searched for genetic variants with a regulatory role in a disease-related tissue, the lip muscle (orbicularis oris muscle [OOM]), of affected individuals. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; SNP genotyping by SNP array

Platforms:

GPL3720 GPL3718 GPL6244

138 Samples

Download data: CEL, CHP

(Submitter supplied) A valuable approach to understand how individual and population genetic differences can predispose to disease is to assess the impact of genetic variants on cellular functions (e.g., gene expression) of cell and tissue types related to pathological states. To understand the genetic basis of nonsyndromic cleft lip with or without cleft palate (NSCL/P) susceptibility, a complex and highly prevalent congenital malformation, we searched for genetic variants with a regulatory role in a disease-related tissue, the lip muscle (orbicularis oris muscle [OOM]), of affected individuals. more...

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array

Platforms:

GPL3720 GPL3718

92 Samples

Download data: CEL, CHP

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by SNP array

Platforms:

GPL570 GPL3720 GPL3718

395 Samples

Download data: CEL

(Submitter supplied) To find BRCA1-associated copy number abberations, the copy number profiles of Familial Basal-like BRCA1-mutated breast carcinomas were compared to Familial Basal-like carcinomas with no pathgogenic BRCA1/2 mutation. This led to the observation of unanticipated heterogeneity of the BRCA1 associated copy number profiles. Gene expression analysis on the same samples identified tumor infiltrating lymphocytes to be responsible for this observation. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL3720 GPL3718

240 Samples

Download data: CEL

(Submitter supplied) Somatic cells can be reprogrammed to a pluripotent state by nuclear transfer into oocytes, yet developmental arrest often occurs. While incomplete transcriptional reprogramming is known to cause developmental failure, reprogramming also involves concurrent changes in gene expression, cell cycle progression and nuclear structure. Here we study cellular reprogramming events in human and mouse nuclear transfer (NT) embryos prior to embryonic genome activation. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL3718

16 Samples

Download data: CEL, CNT

(Submitter supplied) Genome-wide homozygosity mapping was employed for identification of the locus involved in autosomal recessive muscular dystrophy highly prevalent in a small community.

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array

Platform:

GPL3718

1 Sample

Download data: CEL

(Submitter supplied) Non-small cell lung cancer (NSCLC) presents a notoriously genomically unstable cancer type, with numerous large scale and focal genomic aberrations resulting in gene copy number variations across the whole genome. The relations of these gene copy number changes to subsequent mRNA levels are only fragmentarily understood. The aim of this study was an integrated analysis of gene copy number changes and corresponding gene expression in a large clinically annotated NSCLC patient cohort. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL3718

190 Samples

Download data: CEL

(Submitter supplied) Ovarian development and maintenance are poorly understood, but diseases affecting them can offer insights into their underlying mechanisms. XX-female gonadal dysgenesis (XX-GD) is a rare, genetically heterogeneous disorder characterized by underdeveloped, dysfunctional ovaries with subsequent lack of spontaneous pubertal development, primary amenorrhea, uterine hypoplasia, and hypergonadotropic hypogonadism. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL3718

2 Samples

Download data: CEL

(Submitter supplied) Sacrocolpopexy has been dubbed the “gold standard” repair for apical pelvic organ prolapse (POP). This study sought to determine a genetic cause for sacrocolpopexy failure by comparing genotypes from 10 women who suffered from early POP reoccurance after sacrocolpopexy surgery, versus 40 randomly selected women with long term success after the same procedure. We objectively defined early overt failure after robotic-assisted laparoscopic sacrocolpopexy as having a pelvic organ prolapse quantification system examination (POP-Q) of stage III or IV occurring in more than one compartment within six months after surgery. more...

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array

Platform:

GPL3718

50 Samples

Download data: CEL, CHP

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

Organism:

Homo sapiens

Type:

Expression profiling by array; SNP genotyping by SNP array; Genome variation profiling by SNP array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL3718 GPL11154 GPL6244

27 Samples

Download data: BED, BW, CEL, WIG

(Submitter supplied) The mechanistic links between transcription factors and the epigenetic landscape, which coordinate the deregulation of gene networks during cell transformation are largely unknown. We used an isogenic model of stepwise tumorigenic transformation of human primary cells to monitor the progressive deregulation of gene networks upon immortalization and oncogene-induced transformation. By combining transcriptome and epigenome data for each step during transformation and by integrating transcription factor (TF) - target gene associations, we identified 142 TFs and 24 chromatin remodelers/modifiers (CRMs), which are preferentially associated with specific co-expression paths that originate from deregulated gene programming during tumorigenesis. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL3718

3 Samples

Download data: CEL, TXT

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

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; Expression profiling by array

Platforms:

GPL570 GPL3718

319 Samples

Download data: CEL

(Submitter supplied) Nuclear abnormalities are commonly found in human IVF embryos and are associated with DNA damage, aneuploidy, and decreased developmental potential.

Organism:

Homo sapiens

Type:

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

Platform:

GPL3718

72 Samples

Download data: CEL, CHP, TXT