Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide copy number profiling of 18 gastric cancer cell lines using 500K SNP arrays

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE51074 | GEO | 2015/08/04

SECONDARY ACCESSION(S): PRJNA221119

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Copy number profiling of 36 ovarian tumors on Affymetrix 100K SNP arrays and 16 ovarian tumors on 500K SNP arrays

2010-12-16 | GSE26075 | GEO

Affymetrix 500K Mapping Array data from ovary tumors

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

Affymetrix 500K Mapping Array data from breast tumors

Project description:Fifty-one breast tumors were profiled for copy-number alterations with the high-resolution Affymetrix 500K Mapping Array. Combined analysis of the prevalence and amplitude of copy-number alterations defined regions of recurrent gain or loss. Gains were most frequently observed on chromosomes 1, 8, 10, 11, 13, 15, 17, and 20. Losses were most frequent on chromosomes 3, 6, 11, 13, 14, 16, and 17. Compared with previous lower-resolution data, our analysis provided significantly more precise boundaries for frequently altered regions, greatly reducing the number of potential alteration-driving genes. Keywords: Mapping Array

2008-03-17 | GSE7545 | GEO

Copy number profiling of 36 ovarian tumors on Affymetrix 100K SNP arrays and 16 ovarian tumors on 500K SNP arrays

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

Gastric cancer tumor tissue samples and cell lines vs normal sample

Project description:We analyzed DNA copy number alterations in 64 human gastric cancer samples and 8 gastric cancer cell lines using bacterial artificial chromosome (BAC) arrays based comparative genomic hybridisation (aCGH).

2012-11-05 | GSE33501 | GEO

Copy number profiling of gastric cancer cell lines and gastric tumor tissues

Project description:Copy number profiling of 27 gastric cancer cell lines and 105 gastric tumor tissues. we hypothesized that a detailed fine-scale survey of genomic CNAs might reveal potential genes disrupted by fusion events in gastric cancer. We inferred the locations of likely chromosomal breakpoints by identifying regions where closely-spaced microarray probes exhibited striking transitions in copy number. 27 gastric cancer cell lines and 105 gastric tumor tissues were profiled by Agilent 244K microarray.

2010-12-31 | E-GEOD-22694 | biostudies-arrayexpress

Gastric cancer tumor tissue samples and cell lines vs normal sample

2012-11-05 | E-GEOD-33501 | biostudies-arrayexpress

Homo sapiens

Project description:Genome-wide copy number profiling of 18 gastric cancer cell lines using 500K SNP arrays

| PRJNA221119 | ENA