GEO DataSets

(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:

GPL15520 GPL21697 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

(Submitter supplied) T-cell lymphoblastic lymphoma T-LBL is a rare aggressive neoplasm of precursor T cells whose pathogenesis is not fully elucidated and it is closely related to acute lymphoblastic leukemia (T-ALL), the most common subtype of cancer in children, although recent studies suggest biological differences between the two entities.

Organism:

Homo sapiens

Type:

Genome variation profiling by array; Genome binding/occupancy profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL16131

23 Samples

Download data: CEL, CYCHP, XLSX

(Submitter supplied) R-CHOP standard chemotherapy is successful in about 60% of patients with diffuse large B-cell lymphoma (DLBCL). Patients who do not benefit from it, due to tumor drug resistance, have a poor prognosis. To date, the available predictive biomarkers mainly relate to prognosis. We conducted the first prospective GWAS clinical study appositely designed to identify constitutional biomarkers predictive of R-CHOP efficacy and toxicity. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL28377

185 Samples

Download data: CEL, TXT

(Submitter supplied) Objective: The study compared the incidence of aneuploidy and copy number variations (CNVs) in fetuses with increased nuchal translucency (NT) to those with clear indications for non-invasive prenatal screening (NIPS), aiming to evaluate the risk of routine aneuploidy (RA) and pathogenic submicroscopic abnormalities and the potential use of NIPS for fetuses with increased NT. Methods: The study retrospectively analyzed 716 pregnant women with isolated increased NT in Group IiNT and 2960 pregnant women in the control group. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL18637

129 Samples

Download data: CEL, CYCHP

(Submitter supplied) With an escalating global burden, T2DM is associated to long-term complications that have contributed to the burden of morbidity and mortality worldwide. The objective of this manuscript is to conduct an Exome-Wide Association Study (EWAS) on T2DM Emirati individuals to improve our understanding on diabetes-related complications for a more enhanced disease management and improve therapeutic targets.

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array

Platform:

GPL26511

310 Samples

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; 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