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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by SNP array

Platforms:

GPL16131 GPL23159

19 Samples

Download data: CEL, CHP, CYCHP

(Submitter supplied) In this study we present a thus far undescribed, reciprocal, unbalanced chromosomal translocation between the long arm of chromosome 21 and the short arm of chromosome X, t(X;21)(p11.4;q22.12), in five cases with Myelodysplastic Syndromes and Acute Myeloid Leukemias (MDS/AML). The translocation was isolated or accompanied by one additional change and is not generating a fusion gene. Deletion of RUNX1 at chromosome 21 and of BCOR at chromosome X was shown by Fluorescence In Situ Hybridization (FISH) and Single Nucleotide Polymorphism array (SNPa) analysis. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL16131

4 Samples

Download data: CEL, CYCHP

(Submitter supplied) Background: Chromosomal 16p11.2 deletions and duplications are genomic disorders which are characterized by neurobehavioral abnormalities, obesity, congenital abnormalities and so on. However, the prenatal phenotypes of 16p11.2 copy number variations (CNVs) are still not well described till now. This study aimed to provide an elaborate summary of intrauterine phenotypic features for such genomic disorders. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL18637

20 Samples

Download data: CEL

(Submitter supplied) The Barcelona Robertsonian system (BRbS) presents mice with standard karyotype (diploid number 40) but also carrying Robertsonian fusions (ehich lead to variable diploid numbers ranging from 28 to 39). To study the heterogeneity of their genetic background and possible genome divergence between them, samples from three populations were genotyped.

Organism:

Mus musculus; Mus musculus domesticus

Type:

Genome variation profiling by array

Platform:

GPL34100

24 Samples

Download data: IDAT, TXT

(Submitter supplied) Aneuploidy is prevalent in cancer, conferring fitness advantage, multidrug resistance, and poor prognosis. In contrast, experimentally induced aneuploidy often results in adverse effects and impaired proliferation. This paradox underscores the necessity of cancer cells to adapt to abnormal chromosome numbers. To identify molecular mechanisms of adaptation to aneuploidy, we initiated in vitro evolution of cells with extra chromosomes added via microcell-mediated chromosome transfer. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL10123 GPL5477

13 Samples

Download data: TXT

(Submitter supplied) We applied DNA content based flow cytometry methods to interrogate the genomes of clinical samples from 21 patients with early onset colorectal carcinoma (EOCRC). These included a fresh frozen sample obtained from a surgical resection and 20 archived formalin fixed paraffin embedded (FFPE) samples from a Mayo Clinic tissue bank. Our flow sorting methods are compatible with analyses of biopsies of interest including FFPE samples and frozen biopsies. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL19387

7 Samples

Download data: TXT

(Submitter supplied) Using Fluorescence in situ hybridization (FISH), Comparative genomic hybridization on array (aCGH) and Targeted RNA sequencing (RNASeq), we observed a novel fusion of ALK with RPBJ that was amplified and immunohistochemically overexpressed in both the small sarcomatoid component of a chromophobe renal cell carcinoma (chRCC) and in its lymph node metastasis. The amplified RBPJ::ALK fusion was not detected in the chromophobe component of the primary tumour that harbored chRCC-typical losses of chromosomes 1, 2, 6, 10, 13 and 17. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL21558

3 Samples

Download data: CEL, OSCHP

(Submitter supplied) Regulatory T lymphocytes expressing the transcription factor Foxp3 (Treg) play an important role in the prevention of autoimmune diseases and other immunopathologies. Aberrations in Treg-mediated immunosuppression are therefore thought to be involved in the development of autoimmune pathologies but few have been documented. Recent reports indicated a central role for Treg developing during the neonatal period in the prevention of autoimmune pathology. more...

Organism:

Mus musculus

Type:

Genome variation profiling by array

Platform:

GPL34100

96 Samples

Download data: IDAT

(Submitter supplied) This study aimed to evaluate single nucleotide substitutions in mtDNA and analyze their correlation with inflammatory biomarkers in elderly COVID-19 patients. A total of 30 COVID-19 patients and 33 older adult controls (aged over 65 years) were enrolled. mtDNA was extracted from buffy coat samples and sequenced using a chip-based resequencing system (Affymetrix MitoChip v2.0) which detects both homoplasmic and heteroplasmic mtDNA mutations, and allows the assessment of low-level heteroplasmy. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10983

63 Samples

Download data: CEL, CHP

(Submitter supplied) Analysis of Copy Number for bladder cancer using Agilent Human Genome CGH Microarray Kit 4x44K

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL8841

65 Samples

Download data: TXT

(Submitter supplied) Divergence of K-562 genomes through in vitro clonal evolution revealed by comparing three sublines. Comparison of three K-562 sublines

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL16131

3 Samples

Download data: CEL, CYCHP

(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) The duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a type of complex genomic rearrangement (CGR). Although it has been identified as an important mutation signature of pathogenicity for genomic disorders and cancer genomes, its architecture remains unresolved. Here we studied the genomic architecture of DUP-TRP/INV-DUP by investigating the DNA of 24 patients identified by array comparative genomic hybridization (aCGH) on whom we found evidence for the existence of 4 out of 4 predicted structural variant (SV) haplotypes. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platforms:

GPL34013 GPL34011

12 Samples

Download data: TXT

(Submitter supplied) We evaluated 6 established ostesarcoma cell lines. Copy Number Variation and loss-of-heterozygosity status were explored to look for similar patterns across cell lines

Organism:

Homo sapiens

Type:

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

Platform:

GPL16131

6 Samples

Download data: CEL, CYCHP

(Submitter supplied) Genetic variations in drug metabolising enzymes play a role in how individuals respond to drugs. Pharmacogene variation data in the Ghanaian population is limited and this study looks at exploring common variations that exist in our population for commonly used drugs. Samples were validated with PCR-RFLP for accuracy

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL33422

100 Samples

Download data: TXT, XML

(Submitter supplied) HRD Score was generated from a penile carcinoma cell line resistant to 5FU and CDDP as well as cross resistant cell line.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL18602

5 Samples

Download data: CEL, OSCHP

(Submitter supplied) Pregnancy loss is often caused by chromosomal abnormalities of the conceptus. The prevalence of these abnormalities and the allocation of (ab)normal cells in embryonic and placental lineages during intrauterine development remain elusive. We analyzed 1,745 spontaneous pregnancy losses and found that roughly half (50.4%) of the products of conception (POC) were karyotypically abnormal, with maternal and paternal age independently contributing to the increased genomic aberration rate in pregnancy loss. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL21145 GPL28939

463 Samples

Download data: IDAT