Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA129833 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE20355: BAC-microarrays aCGH data from 67 Ewing's Sarcoma tumor samples and 16 Ewing's Sarcoma cell lines GSE20356: Evaluation of copy number alterations in the Ewing's Sarcoma cell line SKES1 with Affymetrix 500k SNP microarray GSE20357: Expression data from DTL silenced-Ewing Sarcoma's cell lines along with their controls Refer to individual Series
2011-07-31 | E-GEOD-20368 | biostudies-arrayexpress
Project description:Copy number profiling of 36 ovarian tumors on Affymetrix 100K SNP arrays Thirty-six ovarian tumors were profiled for copy-number alterations with the Affymetrix 100K Mapping Array. Copy number profiling of 36 ovarian tumors on Affymetrix 500K SNP arrays Sixteen ovary tumors were profiled for copy-number alterations with the high-resolution Affymetrix 500K Mapping Array.
2010-12-16 | GSE26075 | GEO
Project description:The genomic loci with copy number alterations are known to harbor cancer genes. We investigated a comprehensive panel of gastric cancer cell lines for their genome-wide copy number alterations. Eighteen gastric cancer cell lines were profiled using Affymetrix 500K SNP arrays. For copy number calculation, seven independent normal blood samples were profiled together. The copy numbers were calculated genome-wide, in these cell lines with high resolution and reveal the cell line specific amplification and copy number changes.
2015-08-04 | GSE51074 | GEO
Project description:Ewing sarcoma is one of the solid tumor that developed in children. We performed SNP-chip analysis against 27 specimens of Ewing sarcoma using Affymetrix GeneChip and CNAG/AsCNAR software. Our study revealed the detailed profile of copy number alterations in Ewing sarcoma. Keywords: SNP-chip
2010-04-01 | GSE15696 | GEO
Project description:sPNETs are highly malignant embryonal brain tumours of poor prognosis. The underlying biology is poorly understood. To address this we therefore performed high resolution genetic analysis. 36 CNS PNETs and 8 PBs were analysed using the Affymetrix 100K and 500K Mapping Set to identify copy number imbalance at both the chromosome and gene level. Keywords: Affymetrix 100K SNP array, Affymetrix 500K SNP arrays
2011-08-22 | GSE12370 | GEO
Project description:Fifty-seven ovary tumors were profiled for copy-number alterations with the high-resolution Affymetrix 500K Mapping Array. Keywords: Mapping Array
2009-05-18 | GSE11960 | GEO
Project description:Ewing sarcoma is one of the solid tumor that developed in children. We performed SNP-chip analysis against 27 specimens of Ewing sarcoma using Affymetrix GeneChip and CNAG/AsCNAR software. Our study revealed the detailed profile of copy number alterations in Ewing sarcoma. Keywords: SNP-chip To identify oncogenic lesions in Ewing sarcoma, we performed a genome-wide analysis of Ewing sarcoma samples using high-density SNP arrays (Affymetrix GeneChip).
2010-04-01 | E-GEOD-15696 | biostudies-arrayexpress
Project description:Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved HNSCC samples. Copy number analysis of Affymetrix 500K SNP arrays was performed for 11 HNSCC samples, which were used as references for copy number inference.
2016-03-29 | E-GEOD-74555 | biostudies-arrayexpress
Project description:Copy number profiling of 36 ovarian tumors on Affymetrix 100K SNP arrays Thirty-six ovarian tumors were profiled for copy-number alterations with the Affymetrix 100K Mapping Array. Copy number profiling of 36 ovarian tumors on Affymetrix 500K SNP arrays Sixteen ovary tumors were profiled for copy-number alterations with the high-resolution Affymetrix 500K Mapping Array. Affymetrix 100K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization. Each probe set was mapped to the genome, NCBI assembly version 36, using annotation provided by the Affymetrix web site. The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment. Copy number was calculated as power(2,log2ratio + 1). Affymetrix 500K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization. Forty-eight normal samples were downloaded from the Affymetrix website (http://www.affymetrix.com/support/technical/byproduct.affx?product=500k) and analyzed at the same time. One CEL file for each set (Sty and Nsp) with the median signal intensity across the set was selected as the reference array. The dChip-normalized signal intensities were converted to log2 ratios and segmented as follows. For each autosomal probe set, the log2 tumor/normal ratio of each tumor sample was calculated using the average intensity for each probe set in the normal set. For Chromosome X, the average of the 20 normal female samples was used. Each probe set was mapped to the genome, NCBI assembly version 36, using annotation provided by the Affymetrix web site. The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment. Copy number was calculated as power(2,log2ratio + 1).
2010-12-16 | E-GEOD-26075 | biostudies-arrayexpress
Project description:Development of a clinically relevant animal models of RCC for preclinical investigations. For DNA copy number analysis, the Sty I (250K) SNP array of the 500K Human Mapping Array (Affymetrix) was used. Arrays were scanned by GeneChip Scanner 3000 7G. Probe-level signal intensities were normalized to a baseline array with median intensity using invariant set normalization and SNP-level signal intensities were obtained using a model-based (PM/MM) method. Keywords: SNP array data, renal cell carcinoma
2011-05-05 | GSE29062 | GEO