GEO DataSets

(Submitter supplied) Array comparative genomic hybridization data for 372 diagnosis pediatric acute lymphoblastic leukemia samples.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10150

372 Samples

Download data: TXT

(Submitter supplied) Ovarian cancer is a global problem, is typically diagnosed at a late stage and has no effective screening strategy. Platinum-based chemotherapy or Poly(ADP-ribose) polymerase inhibitors (PARPis) treatment are most frequently applied for ovarian cancer patients who are inoperable and in the advanced stage. The recognition of homologous recombination deficiency (HRD) as a biomarker to predict the effect of Platinum-based or PARPis treatment. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL21558

27 Samples

Download data: CEL, OSCHP

(Submitter supplied) Ribosomal DNA (rDNA) is organized as large arrays of tandem repeats that vary in copy number from a few dozen to hundreds. In the budding yeast Saccharomyces cerevisiae, each rDNA repeat includes a potential origin of replication. Previous work has led to the model that the rDNA replication origins compete for limiting replication initiation factors with origins in the rest of the genome, suggesting that reduction in rDNA copy number would reduce competition for these limiting factors and therefore promote origin usage in the rest of the genome. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10930

11 Samples

Download data: TXT

(Submitter supplied) Human induced pluripotent stem cells (iPSCs) provide a virtually inexhaustible source of starting material for cell therapies, such as next generation mesenchymal stem/stromal cells (i.e., iPSC-MSCs), offering an increased clinical efficacy in a variety of diseases. In particular, iPSC-derived products are relevant for treating pathologies in pediatric patients, due to the limited amount of biological material that is easily accessible in infants, toddlers, or young children. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL18637

4 Samples

Download data: CEL, CYCHP

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL33111

39 Samples

Download data: CEL, MTX, TBI, TSV, VCF

(Submitter supplied) The mechanisms by which DNA alleles contribute to disease risk, drug response, and other human phenotypes are highly context-specific, varying across cell types and under different conditions. Human induced pluripotent stem cells (hiPSCs) are uniquely suited to study these context-dependent effects, but to do so requires cell lines from hundreds or thousands of individuals. Village cultures, where multiple hiPSC lines are cultured and differentiated in a single dish, provide an elegant solution for scaling hiPSC experiments to the necessary sample sizes required for population-scale studies. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL33111

20 Samples

Download data: CEL, TBI, VCF

(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; Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL16104

110 Samples

Download data: IDAT

(Submitter supplied) Genomic DNA was extracted from human islets using Dneasy Blood & Tissue Kit (QIAGEN) with RNase A treatment. 200-500ng DNA was genotyped using InfiniumOmni2-5-8v Genotyping BeadChips (Illumina).DNA was isolated from human islet cells from various donors. DNA was genotyped using Illumina Infinium whole-genome genotyping array. Genotypes were called with GenomeStudio (v.2.0.4) using default settings. Genotypes that passed quality filters (missing<0.05, minor allele frequency (MAF>0.01), non-ambiguous alleles defined by AT/GC variants with MAF>40%) were exported.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL16104

36 Samples

Download data: IDAT

(Submitter supplied) Eucalyptus urophylla is a commercially important wood crop plantation species due to its rapid growth, biomass yield, and use as bioenergy feedstock. We characterized the genetic diversity and population structure of 332 E. urophylla individuals from 19 geographically defined E. urophylla populations with a reliability of 14,468 single nucleotide polymorphisms (SNPs). We compared the patterns of genetic variation among these 19 populations. more...

Organism:

Eucalyptus urophylla

Type:

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

Platform:

GPL28143

382 Samples

Download data: IDAT, TXT

(Submitter supplied) The phenotypes of Xp22.33 or Yp11.32 microdeletions containing short-stature homeobox (SHOX) gene have been extensively described in adults and children, however, few have been reported in prenatal fetuses. We analyzed the prenatal ultrasound phenotype and pregnancy outcomes of fetuses with Xp22.33 or Yp11.32 microdeletion containing SHOX gene to improve the understanding, diagnosis, and monitoring of the disease in the fetal period.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL18637

5 Samples

Download data: CEL, CYCHP

(Submitter supplied) Calorie restriction (CR) is known to decrease not only spontaneous but also chemical carcinogen and radiation-induced carcinogenesis. However, the biological mechanisms for the anti-cancer effect of CR remain unclear. In this study, analyzed and compared with genomic alterations in thymic lymphoma (TL) arising after irradiation between with or without CR. The frequency of point mutations at Pten locus on chromosome 19 was not different between 95 kcal and 65 kcal groups, but the frequency of LOH with DNA copy number change in 65 kcal group tended to be higher than 95 kcal group. more...

Organism:

Mus musculus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL19767

48 Samples

Download data: TXT

(Submitter supplied) Intraperitoneal administration of crocidolite or chrysotile is an established method to induce peritoneal malignant mesothelioma(MM), which shares common genetic alterations to those in humans. We conducted high-resolution microarray comparative genomic hybridization mesothelioma tissues obtained from both wild-type and BRCA1+/- rats to evaluate the involvement of BRCA1 haploinsufficiency in carcinogenesis.

Organism:

Rattus norvegicus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10451

16 Samples

Download data: TXT

(Submitter supplied) Multiple variations in olfactory receptor genes are contributing to ASD in females of Arab origin

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL31039

73 Samples

Download data: IDAT, TXT

(Submitter supplied) We introduce a method for generating transgene-free and high-quality naive human induced pluripotent stem cells (iPSCs) using a modified Sendai virus (SeV) vector reprogramming system. This reprogramming method realizes the derivation of naive iPSCs from various somatic cells accompanied with fast and robust SeV vector removal at early passages. The established naive iPSCs have superior differentiation ability compared with iPSCs derived from conventional methods.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL32421

11 Samples

Download data: IDAT, TXT

(Submitter supplied) Background: Ovarian clear cell carcinomas (OCCCs) are rare, aggressive and chemoresistant tumors. Geographical and ethnic differences in the incidence of OCCC have been reported with a higher incidence in Asiatic countries. There is a paucity of information regarding OCCC in Latin America (LA) and other countries. Methods: Here, we characterized two cohorts of 33 patients with OCCC from LA (24 from Brazil and 9 from Costa Rica) and a cohort of 27 patients from Spain. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL21558

27 Samples

Download data: CEL, OSCHP, TXT

(Submitter supplied) The 1986 Chernobyl nuclear disaster initiated a series of catastrophic events resulting in long-term and widespread environmental contamination. We characterize the genetic structure of 302 dogs representing three free-roaming dog populations living within the power plant itself, or 15-45 km from the disaster site. Genome-wide profiles from Chernobyl, purebred, and free-breeding dogs world-wide reveal that the individuals from the power plant and Chernobyl City are genetically distinct, with the former displaying increased intrapopulation genetic similarity and differentiation. more...

Organism:

Canis lupus familiaris

Type:

Genome variation profiling by SNP array

Platform:

GPL17481

299 Samples

Download data: BED, BIM, FAM, IDAT, TXT

(Submitter supplied) Cytogenetics abnormalities (CA) are known to be the preponderant prognostic factor in multiple myeloma (MM). Our team has recently developeda prognostic score based on 6 CA, where del(1p32) appears to be the second worst abnormality after del(17p). The aim of this study was to confirm the adverse impact of 1p32 deletion on newly-diagnosed multiple myeloma (NDMM) patients. Among 2551 NDMM patients, 11% were harboring del(1p32). more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL16131

1395 Samples

Download data: CEL, CYCHP

(Submitter supplied) we used single-cell transcriptomics and genotyping arrays to characterize 17 neuroblastoma samples across different risk groups and genetic subsets.Fresh samples, obtained from surgical resections and core biopsies, were used for genome variation profiling. DNA extraction from neuroblastoma samples was performed using the DNeasy blood and tissue kit (Qiagen) according to the manufacturer’s protocol. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL16131

17 Samples

Download data: CEL

(Submitter supplied) To investigate DNA copy number changes in mouse B-cell lymphoma induced by ionizing radiation.

Organism:

Mus musculus

Type:

Genome variation profiling by array

Platform:

GPL19767

9 Samples

Download data: TXT, XLSX

(Submitter supplied) Comparative genomic hybridization experiments comparing DNA from experimentally evolved yeast strains to DNA from a euploid control.

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by array

Platform:

GPL4131

12 Samples

Download data: TXT