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Array-based comparative genomic hybridization analysis of primary neuroblastoma

ABSTRACT: We conducted microarray-based comparative genomic hybridization (array-CGH) with a DNA chip carrying 2,464 BAC clones to examine genomic aberrations of 236 neuroblastomas (112 sporadic and 124 mass screening-detected). In paralell, gene-expression profiling was also performed by using in-house cDNA microarrays. Keywords: Comparative genomic hybridization

ORGANISM(S): Homo sapiens

PROVIDER: GSE5784 | GEO | 2007/08/06

SECONDARY ACCESSION(S): PRJNA97137

REPOSITORIES: GEO

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Array-based comparative genomic hybridization analysis of primary neuroblastoma

Project description:We conducted microarray-based comparative genomic hybridization (array-CGH) with a DNA chip carrying 2,464 BAC clones to examine genomic aberrations of 236 neuroblastomas (112 sporadic and 124 mass screening-detected). In paralell, gene-expression profiling was also performed by using in-house cDNA microarrays. Keywords: Comparative genomic hybridization A UCSF BAC array carrying 2,464 clones, which covers the whole human genome at roughly 1.2-Mb resolution, was used. The 500-ng aliquots of tumors and reference DNAs were labeled by random priming with each Cy3-dCTP and Cy5-dCTP (Amersham Pharmacia, Piscataway, NJ). Hybridization was performed as previously reported [Pinkel D, et al. Nat Genet 1998;20:207-11.]. UCSF Spot and UCSF Sproc programs to analyze values for spotted clones [Jain AN, et al. Genome Res 2002;12:325-32.] were used.

2007-08-06 | E-GEOD-5784 | biostudies-arrayexpress

Gene expression profiling of sporadic neuroblastoma

Project description:Integrated analysis of array-based comparative genome hybridization (aCGH) and gene expression profiling was conducted by using primary neuroblastomas. This submission corresponds the latter gene expression data. Keywords: other Thirty mass screening-detected and 40 sporadic neuroblastomas were analyzed by both aCGH and gene expression profiling. A UCSF BAC array carrying 2,464 clones was used for the former experiment. For the latter experiment, an in-house cDNA microarray, carrying 5,340 cDNAs obtained from the oligo-capping cDNA libraries generated from anonymous neuroblastoma tissues, were used. Preparation of RNA, hybridization, reading of spots, and statistical analyses were conducted as reported previously [Ohira M, et al. Cancer Cell 2005;7:337-50.]. This series corresponds expression profiles for 40 sporadic neuroblastomas.

2007-09-05 | E-GEOD-5779 | biostudies-arrayexpress

SKOV3 cells comparative genomic hybridization

Project description:SKOV3 cells comparative genomic hybridization using Affymetrix SNP 6.0 microarray

2019-12-16 | GSE53121 | GEO

Heterologous Microarray Hybridization Between Vesicomyid Symbionts

Project description:The goal of this study was to use heterologous microarray hybridization to determine genomic content shared among different vesicomyid symbionts. These symbionts are closely related and can be thought of as different strains of bacteria, facilitating the use of heterologous microarray hybridization to determine genomic content. Keywords: comparative genomic hybridization

2008-11-28 | GSE13447 | GEO

Comparative genomic hybridization study of Streptococcus pneumoniae

Project description:Comparative genomic hybridization study of Streptococcus pneumoniae

| PRJNA141383 | ENA

Comparative genomic hybridization of Shewanella baltica strains

Project description:Comparative genomic hybridization of Shewanella baltica strains

| PRJNA510414 | ENA

Comparative genomic hybridization of human osteosarcoma cell lines

Project description:Comparative genomic hybridisation of 20 osteosarcoma cell lines using a homemade 1 Mb BAC/PAC microarray.

2010-02-10 | E-MEXP-1750 | biostudies-arrayexpress

High-resolution comparative genomic hybridization of inflammatory breast cancer and identification of candidate genes

Project description:Inflammatory breast cancer (IBC) is an aggressive form of BC poorly defined at the molecular level. We compared the molecular portraits of 63 IBC and 134 non-IBC (nIBC) clinical samples. Genomic imbalances of 49 IBCs and 124 nIBCs were determined using high-resolution array-comparative genomic hybridization, and mRNA expression profiles of 197 samples using whole-genome microarrays. Genomic profiles of IBCs were as heterogeneous as those of nIBCs, and globally relatively close. However, IBCs showed more frequent “complex” patterns and a higher percentage of genes with CNAs per sample. The number of altered regions was similar in both types, although some regions were altered more frequently and/or with higher amplitude in IBCs. Many genes were similarly altered in both types; however, more genes displayed recurrent amplifications in IBCs.

2011-03-01 | GSE23720 | GEO

Regeneration of comparative genomic hybridization oligonucleotide microarrays with dimethylurea

Project description:Reuse of materials in DNA hybridization based methods has been known since the advent of Southern membranes. Array based comparative genomic hybridization is essentially Southern hybridization with multiple probes immobilized on a solid surface. We have shown that comparative genomic hybridization microarrays fabricated with maskless array synthesizer technology can be used up to four times with application of 1,3-dimethylurea as array-stripping agent. We reproducibly detected chromosomal aberrations, 0.6 to 22.4 Mb in size, in four hybridization rounds using regenerated microarray slides. We have also demonstrated that regenerated arrays can detect smaller alterations, 16 – 200 kbp, such as common copy number variants, as well as complex aberration profiles in tumor.

2012-05-23 | GSE35740 | GEO

Array-based comparative genomic hybridization study of human embryonic stem cell lines

Project description:G-banding of human embryonic stem cells (hESC) has proved their predisposition to aneuploidy of chromosomes 12, 17 and X. Now, using array-based comparative genomic hybridization, we find that hESC also accumulate other recurrent chromosomal abnormalities, such as duplications of stemness genes, submicroscopic instability of 20q11.21 and the appearance of a derivative chromosome 18. Keywords: comparative genomic hybridization, genomic integrity of human embryonic stem cells

2008-11-04 | GSE13422 | GEO

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