Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of human neuroblastoma cell lines using a dene-resolution analysis method of DNA copy number variation using oligonucleotide expression microarrays

ABSTRACT: 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. Experiment Overall Design: Genomic DNA isolated from peripheral blood samples and from Neuroblastoma cell lines was fragmented by DNAseI and biotin labeled by terminal transferase. Labeled DNAs were hybridized to U133plus2.0 GeneChips (Affymetrix). Hybridization and other conditions were slightly modified from those suggested for 10K Mapping Arrays (Affymetrix) and washing conditions were carried out as suggested for 100K Mapping Arrays. Probe set signals were either generated using the RMA algorithm or using the in-house developed WPP algorithm. Copy-number variation between Neuroblastoma and normal DNA was calculated.

ORGANISM(S): Homo sapiens

SUBMITTER: David Lawrence Newsom

PROVIDER: E-GEOD-7364 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data

Project description:Copy number variants (CNVs) are currently defined as genomic sequences that are polymorphic in copy number and range in length from 1,000 to several million base pairs. Among current array-based CNV detection platforms, long-oligonucleotide arrays promise the highest resolution. However, the performance of currently available analytical tools suffers when applied to these data because of the lower signal:noise ratio inherent in oligonucleotide-based hybridization assays. We have developed wuHMM, an algorithm for mapping CNVs from array comparative genomic hybridization (aCGH) platforms comprised of 385,000 to more than 3 million probes. wuHMM is unique in that it can utilize sequence divergence information to reduce the false positive rate (FPR). We apply wuHMM to 385K-aCGH, 2.1M-aCGH, and 3.1M-aCGH experiments comparing the 129X1/SvJ and C57BL/6J inbred mouse genomes. We assess wuHMM’s performance on the 385K platform by comparison to the higher resolution platforms and we independently validate 10 CNVs. The method requires no training data and is robust with respect to changes in algorithm parameters. At a FPR of less than 10%, the algorithm can detect CNVs with five probes on the 385K platform and three on the 2.1M and 3.1M platforms, resulting in effective resolutions of 24 kb, 2-5 kb, and 1 kb, respectively. Keywords: CNV detection algorithm development and assessment

2008-03-12 | GSE10511 | GEO

Transcription profiling of human peripheral blood mononuclear cells from Africans and Caucasians to analyse gene copy number polymorphism, a major source of genetic variation between humans

Project description:We have performed a genome wide analysis of gene copy number polymorphisms and report here for the first time that the human genome contains thousands of well-characterized genes at copy numbers different from one maternal and one paternal allele; and that, furthermore, the copy numbers of hundreds of well-characterized genes can vary between two normal healthy humans making this a major source of genetic variation. Groups of genes affected by CNPs include genes involved in signal transduction, oncogenesis, cell adhesion activity and several types of immune response. In contrast to SNPs, which preferentially affect non-coding regions of the genome, copy number polymorphisms of well-characterized and actively expressed genes are very likely to have important biological consequences. Experiment Overall Design: We utilized an expression microarray to analyze gene copy number variations (GCNVs).

2008-06-13 | E-GEOD-4981 | biostudies-arrayexpress

wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data

2008-03-11 | E-GEOD-10511 | biostudies-arrayexpress

Chromosome 17/17q gain and unaltered profiles in high resolution array-CGH are prognostically informative in neuroblastoma

Project description:Oligonucleotide aCGH profiles from 37 neuroblastoma tumor samples were generated using 44K or 105K microarrays.

2014-06-01 | GSE56109 | GEO

Genome-wide assessment of DNA aberrations in human neuroblastoma primary tumors using BAC array

Project description:DNA signature patterns embed important prognostic information in diagnostic neuroblastoma samples, and can identify candidate cancer-related genes. Keywords: aCGH

2007-03-10 | GSE7230 | GEO

Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays

Project description: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. Keywords: genomic DNA, CGH, Copy Number Variation

2007-03-29 | GSE7364 | GEO

Hox-C9 activates the intrinsic pathway of apoptosis and is associated with spontaneous regression in neuroblastoma [aCGH_44k]

Project description:Oligonucleotide aCGH profiles from 209 neuroblastoma tumor samples were generated using 44K, 105K or 1M microarrays. The 209th sample is represented by Sample GSM634116.

2013-03-26 | GSE45476 | GEO

Hox-C9 activates the intrinsic pathway of apoptosis and is associated with spontaneous regression in neuroblastoma [aCGH_105k]

Project description:Oligonucleotide aCGH profiles from 209 neuroblastoma tumor samples were generated using 44K, 105K or 1M microarrays. The 209th sample is represented by Sample GSM634116.

2013-03-26 | GSE45478 | GEO

Hox-C9 activates the intrinsic pathway of apoptosis and is associated with spontaneous regression in neuroblastoma [aCGH_1M]

Project description:Oligonucleotide aCGH profiles from 209 neuroblastoma tumor samples were generated using 44K, 105K or 1M microarrays. The 209th sample is represented by Sample GSM634116.

2013-03-26 | GSE45477 | GEO

Chromosome 17/17q gain and unaltered profiles in high resolution array-CGH are prognostically informative in neuroblastoma

Project description:Oligonucleotide aCGH profiles from 37 neuroblastoma tumor samples were generated using 44K or 105K microarrays. Two-color array-based comparative genome hybridization (aCGH)

2014-06-01 | E-GEOD-56109 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data