GEO DataSets

(Submitter supplied) Free-breeding dogs have occupied the Galápagos islands at least since the 1830s, however, it was not until the 1900s that dog populations grew substantially, endangering wildlife and spreading disease. In 1981, authorities sanctioned the culling of free-roaming dogs. Yet there are currently large free-roaming dog populations of unknown ancestry on the islands of Isabela and Santa Cruz, whose ancestry has never been assessed on a genome-wide scale. more...

Organism:

Canis lupus familiaris

Type:

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

Platform:

GPL17481

187 Samples

Download data: IDAT, TXT

(Submitter supplied) Desmoid tumors are bland fibroblastic tumors with little histologic variation in different regions of the tumor. While desmoid tumors do not metastasize, they have a high rate of local recurrence after complete resection and no reliable predictors of clinical behavior exist. The presence of molecular intra- and inter-tumor heterogeneity has been well established in other, higher grade, sarcomas but little is known about molecular variability within histologically bland lesions. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL21558

23 Samples

Download data: CEL, OSCHP

(Submitter supplied) The JGOG3025 study was conducted by the Japanese Gynecologic Oncology Group (JGOG) on 710 patients with epithelial ovarian cancer (NCT03159572). In the JGOG3025-TR2 study, fresh frozen tumor tissues from 274 and 15 cases diagnosed as stage II or higher high-grade serous carcinoma (HGSC) or high-grade endometrioid carcinoma (HGEC) in the central pathological review were submitted to SNP array, total RNA-sequencing, and DNA methylation array analyses.

Organism:

Homo sapiens

Type:

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

Platform:

GPL21558

287 Samples

Download data: CEL, OSCHP, TXT

(Submitter supplied) Background: Vitamin D is associated with lung health in epidemiologi studies, but mechanisms mediating observed associations are poorly understood. This study explores mechanisms for an effect of vitamin D in lung through an in vivo gene expression study, an expression quantitative trait loci (eQTL) analysis in lung tissue, and a population-based cohort study of sequence variants. Methods: Microarray analysis investigated the association of gene expression in small airway epithelial cell with serum 25[OH]D in adult nonsmokers. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL6804 GPL570

142 Samples

Download data: CEL, CHP

(Submitter supplied) Background: Cases where genotype-phenotype relationships depend on environmental factors have been quantified for many complex diseases. Such genotype-environment interactions (GEI or GxE) may also affect expression Quantitative Trait Loci (eQTL) present in tissues critical for the manifestation of disease. To assess this hypothesis, we performed an analysis of eQTL-GEI resulting from an individual's smoking environment in the lung small airway epithelium (SAE). more...

Organism:

Homo sapiens

Type:

Expression profiling by array; SNP genotyping by SNP array

Platforms:

GPL570 GPL6804

180 Samples

Download data: CEL, CHP

(Submitter supplied) Testican 3 (coded for by SPOCK3), is an extracellular matrix heparan/chondroitin sulphate proteoglycan that possesses serine and cysteine protease inhibitor-like domains Based on the knowledge that serine proteases contribute to the destruction of the lung in cigarette smokers, but that only a fraction of smokers develop smoking-induced lung disease, we hypothesized that smokers expressed SPOCK3 at lower levels in the small airway epithelium, the initial site of smoking-induced disease, and further, that genetic variability modulates the expression of SPOCK3 in the airway epithelium. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL570 GPL6804

212 Samples

Download data: CEL, CHP

(Submitter supplied) Human pluripotent stem cells have two major pluripotent states, primed and naive, and the heterogeneity among cell lines in each pluripotent state remains a major unresolved problem. We showed that the overexpression of H1FOO-DD, which has a short expression period by fusing the destabilized domain to the maternal-specific linker histone H1FOO, together with OCT4, SOX2, KLF4 and LMYC in human somatic cells improves the quality of reprogramming to primed and naive pluripotency.

Organism:

Homo sapiens

Type:

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

Platform:

GPL34118

30 Samples

Download data: IDAT, TXT

(Submitter supplied) SNP array data from 45 cell lines of Malignant Pleural Mesothelioma were used to explore recurrent copy number alterations. This study was part of Cartes d'Identité des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer.

Organism:

Homo sapiens

Type:

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

Platform:

GPL21168

45 Samples

Download data: IDAT, TXT

(Submitter supplied) Here, we report on a novel chicken comb phenotype, designated Antler-comb. Using a 600K Axiom® Genome-Wide Chicken Genotyping Array, we separately genotyped 12 and 24 female Hetian Wildtype-comb and Antler-comb chickens, respectively. Meanwhile, we sequenced the genomes of 10 Hetian Antler-comb and 10 Wildtype-comb chickens to interrogate the GWAS results and explore the potential genetic variants underlying this phenotype. more...

Organism:

Gallus gallus

Type:

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

Platform:

GPL23815

36 Samples

Download data: CEL, XLSX

(Submitter supplied) It is unknown whether pediatric monomorphic post-transplant lymphoproliferative disorders (mPTLD) display similar genetic features than the immunocompetent counterpart and if they resemble adult mPTLD. We have investigated 39 pediatric mPTLD, 33 diffuse large B-cell lymphoma (DLBCL) and six Burkitt lymphoma (BL), by an integrated approach, including fluorescence in situ hybridization, cell of origin determination (COO), targeted gene sequencing and copy-number arrays. more...

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL18603 GPL18602

26 Samples

Download data: CEL, OSCHP, XLSX

(Submitter supplied) Background: Most skin-related traits have been studied in Caucasian genetic backgrounds. A comprehensive study on skin-associated genetic effects on underrepresented populations such as Vietnam is needed to fill the gaps in the field. Objectives: We aimed to develop a computational pipeline to predict the effect of genetic factors on skin traits using public data (GWAS catalogs and whole-genome sequencing (WGS) data from the 1000 Genomes Project-1KGP) and in-house Vietnamese data (WGS and genotyping by SNP array). more...

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array

Platform:

GPL33106

96 Samples

Download data: IDAT, VCF

(Submitter supplied) Head and neck squamous cell carcinomas (HNSqCC) are related with cigarette, alcohol and areca quid (AQ). In the era of precision preventive medicine, susceptible genetic markers for HNSqCCs were investigated by genome-wide association manner.

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array

Platform:

GPL32738

698 Samples

Download data: CEL, TXT

(Submitter supplied) Genetic studies have identified numerous loci associated with type 2 diabetes (T2D), but the functional role of many loci has remained unexplored. In this study, we engineered isogenic knockout human embryonic stem cell (hESC) lines for 20 genes associated with T2D risk. We systematically examined β-cell differentiation, insulin production and secretion, and survival. We performed RNA-seq and ATAC-seq on hESC-β cells from each knockout line. more...

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array

Platform:

GPL25201

1 Sample

Download data: IDAT, TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL24676 GPL25201

139 Samples

Download data: IDAT, TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL21697 GPL15520 GPL13829

9 Samples

Download data: IDAT, VCF

(Submitter supplied) Cell replacement therapies for Parkinson’s Disease (PD) based on transplantation of dopaminergic neurons generated from pluripotent stem cell sources are now entering clinical trials.  Here, we present the quality, safety and efficacy data supporting a first-in-human clinical trial in PD using an embryonic stem cell product STEM-PD, as well as the design of the trial itself. The cryopreserved STEM-PD product was manufactured under Good Manufacturing Practice (GMP) and fully quality-tested in vitro for regulatory compliance. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL13829

6 Samples

Download data: CSV, IDAT

(Submitter supplied) Naturally occurring canine invasive urinary carcinoma (iUC) closely resembles human muscle invasive bladder cancer in terms of histopathology, metastases, response to therapy and, low survival rate. The heterogeneous nature of the disease has led to the association of large numbers of risk loci in humans, however most are of small effect. There exists a need for new and accurate animal models of invasive bladder cancer. more...

Organism:

Canis lupus familiaris

Type:

SNP genotyping by SNP array

Platform:

GPL17481

160 Samples

Download data: IDAT, TXT

(Submitter supplied) Here, we show that in hepatocellular carcinoma (HCC, the most prevalent form of primary liver cancer), tumours with a high burden of broad genomic alterations presented immune exclusion. On the other hand, HCC tumours with a reduced rate of broad genomic alterations were enriched in the HCC immune class, exhibited inflammatory traits and were cleared from CTNNB1 mutations. Overall, we propose that, in HCC, the acquisition of high-levels of broad copy number alterations might be implicated in the development of immune evasion, and that tumours presenting a reduced rate of these broad alterations display an immune profile which may indicate a favourable response to immunotherapies.

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array

Platform:

GPL16333

300 Samples

Download data: IDAT, TXT

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

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array; Methylation profiling by genome tiling array; Other

Platforms:

GPL13534 GPL18900

43 Samples

Download data: IDAT

(Submitter supplied) Meningiomas are the most common primary brain tumor. Though typically benign with a low mutational burden, histopathologic analysis has poor predictive value for malignant behavior and there are no proven chemotherapies. Although DNA methylation patterns distinguish subgroups of meningiomas and have higher predictive value for tumor behavior than histologic classification, little is known about differences in DNA methylation between meningiomas and surrounding normal dura tissue. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL18900

19 Samples

Download data: IDAT, TXT