GEO DataSets

(Submitter supplied) Chromosomal regions harboring tumor suppressors and oncogenes are often deleted or amplified. Array comparative genomic hybridization (CGH) detects segmental DNA copy number alterations in tumor DNA relative to a normal control. The recent development of a bacterial artificial chromosome (BAC) array, that spans the human genome in a tiling path manner with >32,000 clones, has facilitated whole genome profiling at an unprecedented resolution. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL2043 GPL2616

28 Samples

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL6947 GPL4723

150 Samples

Download data: GPR

(Submitter supplied) Lung cancer is the worldwide leading cause of death from cancer. This GEO series correspond to one of the BAC aCGH data sets used as validation cohort for the study: Landscape of somatic allelic imbalances and copy number alterations in human lung cancer, Int J Cancer 2013.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4723

78 Samples

Download data: GPR, XLS

(Submitter supplied) BACKGROUND: Cervical carcinoma develops as a result of multiple genetic alterations. Different studies investigated genomic alterations in cervical cancer mainly by means of metaphase comparative genomic hybridization (mCGH) and microsatellite marker analysis for the detection of loss of heterozygosity (LOH). Currently, high throughput methods such as array comparative genomic hybridization (array CGH), single nucleotide polymorphism array (SNP array) and gene expression arrays are available to study genome-wide alterations. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL4012 GPL2641 GPL201

40 Samples

Download data: CEL, GPR

(Submitter supplied) 7 breast cancer cell lines were differentially labeled and each competitively hybridized against female genomic DNA using the 32K SMRT Array Keywords: None

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL2735 GPL2043

7 Samples

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(Submitter supplied) A BAC-array platform for comparative genomic hybridization was constructed from a library of 32,433 clones providing complete genome coverage, and evaluated by screening for DNA copy number changes in 11 breast cell lines (BT474, MCF7, HCC1937, SK-BR-3, L56Br-C1, ZR-75-1, MCF10A, JIMT1, MDA-MB-231, MDA-MB-361 and HCC2218). These were also characterized by gene expression analysis and found to represent all five recently described breast cancer subtypes using the ‘intrinsic gene set’ and centroid correlation. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4723

11 Samples

Download data: TXT

(Submitter supplied) Breakpoint spanning oligonucleotide arrays were designed essentially as described previously (Selzer et al., 2005). Briefly, the regions of interest were repeat-masked. The array design contained both 50-mer fixed length probes and isothermal probes that ranged in length from 45 bp to 77 bp. Probes were generated from both strands, and replicated on the array 3 times. The arrays were constructed by maskless array synthesis technology (NimbleGen Systems Inc.), with up to 385,000 oligonucleotides being synthesized by photolithography. more...

Organism:

Homo sapiens

1 Series

1 Sample

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(Submitter supplied) This series contain 36 samples obtained from human lung tissue and includes the following: 7 Adenocarcinoma samples. 16 Squamous cell carcinoma samples. 1 AdenoSquamous sample. 2 Renal Metastasis. 1 Colon metastasis. 7 normal lung tissue adjacent to the tumors. 2 commercial normal lung RNA. Keywords = Lung Keywords = Non Small Cell Lung Cancer Keywords = Adenocarcinoma Keywords = Squamous Cell Carcinoma Keywords = Normal Lung. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL91

37 Samples

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(Submitter supplied) Genomic changes in chromosome 8 are commonly observed in breast cancer cell lines and tumors. Fine mapping of such genomic changes, and evaluation of associated expression changes, are expected to provide reagents for diagnosis, insights into understanding the disease, and open up avenues for novel therapeutic intervention. We made an effort to search for genes on chromosome 8 with altered copy number and expression. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL4615 GPL4611

42 Samples

Download data: TXT

(Submitter supplied) RNA expression analysis was performed to compare patterns to DNA copy number changes and sensitivity to BCL2 inhibitors. Keywords: cell line comparison

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3029

Platform:

GPL571

34 Samples

Download data: CEL

Analysis of small-cell lung carcinoma cell (SCLC) lines. Expression profiles compared to the cell lines' sensitivity to the Bcl-2 antagonist ABT-737 and chromosomal gains that include changes in Bcl-2 gene copy number. ABT-737 induces the regression of a fraction of SCLC solid tumors.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 cell type, 4 genotype/variation sets

Platform:

GPL571

Series:

GSE7097

34 Samples

Download data: CEL

(Submitter supplied) High-resolution array-CGH was performed to identify differences in the patterns of genomic imbalances between SCC and AC of non-small cell lung cancer (NSCLC). On a genome-wide profile, SCCs showed higher frequency of gains than ACs (p = 0.067). More specifically, statistically significant differences were observed across the histologic subtypes for gains at 2q14.2, 3q26.2-q29, 12p13.2-p13.33, and 19p13.3, as well as losses at 3p26.2-p26.3, 16p13.11, and 17p11.2 in SCC, and gains at 7q22.1 and losses at 15q22.2-q25.2 occurred in AC (P < 0.05). more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL8690

36 Samples

Download data: GPR, TXT

(Submitter supplied) A tiling resolution array of 32,433 overlapping BAC clones spanning the human genome (NOTE: this is the same clone-set as the "BCCRC Lam SMRT array 32k" except that clones with insufficient annotation data have been removed; genome coverage remains the same). Protocol: See PMID: 14981516

Organism:

Homo sapiens

2 Series

23 Samples

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(Submitter supplied) A tiling resolution array of 26, 928 overlapping BAC clones spanning the human genome Keywords = SMRTr tiling array Protocol: N/A

Organism:

Homo sapiens

13 Series

596 Samples

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(Submitter supplied) A tiling resolution array of 32,433 overlapping BAC clones spanning the human genome (NOTE: this is the same clone-set as the "BCCRC Lam SMRT array 32k" except that clones with insufficient annotation data have been removed; genome coverage remains the same). Keywords = SMRT tiling array

Organism:

Homo sapiens

1 Series

2 Samples

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(Submitter supplied) A tiling resolution array of 32,433 overlapping BAC clones spanning the human genome Keywords = SMRT tiling array

Organism:

Homo sapiens

6 Series

80 Samples

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(Submitter supplied) K14Cre; Brca2F/F; p53F/F tumor analysis Keywords: Comparative Genomic Hybridization, aCGH

Organism:

Mus musculus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL2851

4 Samples

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(Submitter supplied) An oligo array based high-resolution analysis of copy number alterations in 171 primary breast tumors of relatively small size and low NPI, and 49 breast cancer cell-lines. Objectives of the study were to study the molecular taxonomy and the genomic aberration patterns in a breast cancer cohort representative of breast cancer demographics. Keywords: array comparative genomic hybridisation

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL5737

220 Samples

Download data: TXT

(Submitter supplied) In cancer, proto-oncogenes are often altered by genomic amplification. Recent studies have highlighted a role for PDGFRA as an oncogene in non-small cell lung cancer. To characterize 4q12 copy number status in NSCLC, both previously published (Weir et al. PMID 17982442) and unpublished Affymetrix 250K SNP array data for 733 NSCLC samples (628 primary samples, 105 cell lines) were evaluated for copy number aberrations. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL3720

30 Samples

Download data: CEL

(Submitter supplied) ULTRA GAPS (Gama Amino Propyl Silane) Protocol: This BAC array platform consisted of 3315 unique BACs spotted in-house on CorningCMT Ultra-Gap slides (Corning, USA) using two replicates printed on each slide. Details of array construction are described elsewhere (Greshock et al., 2004) Greshock J, Naylor TL, Margolin A, Diskin S, Cleaver SH, Futreal PA, deJong PJ, Zhao S, Liebman M, Weber BL. 2004. 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. Genome Res 14(1):179-87.

Organism:

Homo sapiens

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