GEO DataSets

(Submitter supplied) The arrays contain 2464 BAC clones printed as triplicate spots and are described in: Snijders AM, Nowak N, Segraves R, et al. Assembly of microarrays for genome-wide measurement of DNA copy number. Nature Genetics 2001; 29:263-264. Protocol: http://cancer.ucsf.edu/array

Organism:

Homo sapiens

3 Series

161 Samples

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(Submitter supplied) This series represents the data set from the paper <u>Assembly of microarrays for genome-wide measurement of DNA copy number</u> appearing in Nat Genet 2001 Nov;29(3):263-4 and it's web supplement. Specimen procurement, labeling, hybridization and imaging protocols from Nat Genet 2001 Nov;29(3):263-4 web supplement: <b>Specimens.</b> We obtained GM03563, GM00143, GM05296, GM07408, GM01750, GM03134, GM13330, GM03576, GM01535, GM07081, GM02948, GM04435, GM10315, GM13031 and GM01524 cell strains from the NIGMS Human Genetics Cell Repository (Coriell Institute for Medical Research), and cultured them under the recommended conditions. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL28

25 Samples

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(Submitter supplied) The arrays contain 2464 BAC clones printed as triplicate spots and are described in: Snijders AM, Nowak N, Segraves R, et al. Assembly of microarrays for genome-wide measurement of DNA copy number. Nature Genetics 2001; 29:263-264. Protocol: http://cancer.ucsf.edu/array

Organism:

Homo sapiens

2 Series

20 Samples

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(Submitter supplied) The arrays contain 2462 BAC clones printed as triplicate spots and are described in: Snijders AM, Nowak N, Segraves R, et al. Assembly of microarrays for genome-wide measurement of DNA copy number. Nature Genetics 2001; 29:263-264.

Organism:

Homo sapiens

2 Series

142 Samples

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(Submitter supplied) This array was designed for copy-number assessments across the human genome. We printed 2,460 BAC and P1 clones in triplicate (approx. 7,500 elements) in a 12mm X 12mm square. Each clone contains at least one STS, allowing linkage to the genome sequence. Cytogenetic mapping indicated that 2,298 of the arrayed clones are single copy; this array thus provides average resolution of approximately 1.4 Mb across the genome. more...

Organism:

Homo sapiens

2 Series

61 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) Gene amplifications and deletions frequently contribute to tumorigenesis. Characterization of these DNA copy-number changes is important for both the basic understanding of cancer and its diagnosis. Comparative genomic hybridization (CGH) was developed to survey DNA copy-number variations across a whole genome. With CGH, differentially labelled test and reference genomic DNAs are co-hybridized to normal metaphase chromosomes, and fluorescence ratios along the length of chromosomes provide a cytogenetic representation of DNA copy-number variation. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL179

10 Samples

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(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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(Submitter supplied) ULTRA GAPS (Gama Amino Propyl Silane) Protocol: This BAC array platform consisted of 4575 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

Download data

(Submitter supplied) ULTRA GAPS (Gama Amino Propyl Silane) Protocol: This BAC array platform consisted of 4798 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

Download data

(Submitter supplied) Ultra GAPS (Gama Amino Propyl Silane) Protocol: This BAC array platform consisted of 5217unique 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. more...

Organism:

Homo sapiens

Download data

(Submitter supplied) ULTRA GAPS (Gama Amino Propyl Silane) Protocol: This BAC array platform consisted of 5215 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. more...

Organism:

Homo sapiens

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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) 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) We present a novel method of using commercial oligonucleotide expression microarrays for aCGH, enabling DNA copy number measurements and expression profiles to be combined using the same platform. This method yields aCGH data from genomic DNA without complexity reduction at a median resolution of approximately 17,500 base pairs. Due to the well-defined nature of oligonucleotide probes, DNA amplification and deletion can be defined at the level of individual genes and can easily be combined with gene expression data. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL570

8 Samples

Download data: CEL

(Submitter supplied) An array CGH hybridization of breast cancer cell line T47D compared against a normal human female reference.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4091

1 Sample

Download data: 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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