Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Regeneration of comparative genomic hybridization oligonucleotide microarrays with dimethylurea

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE35740 | GEO | 2012/05/23

SECONDARY ACCESSION(S): PRJNA152029

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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 M-bM-^@M-^S 200 kbp, such as common copy number variants, as well as complex aberration profiles in tumor. Peripheral blood leukocyte DNA samples from 7 individuals with subchromosomal aberrations vs a pool of female DNA (Promega). The experiments were performed in quadruplicate on succesively regenerated microarrays. One dye swap was performed..

2012-05-22 | E-GEOD-35740 | biostudies-arrayexpress

ENCODE ChIP-chip for STAT1 on Human Hela S3 Cells

Project description:STAT1 ChIP-chip performed on Human Hela S3 Cells for three different platforms. Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts) (5 biological replicates), custom maskless array tiling most of ENCODE with 50mer oligonucleotides end-to-end (3 biological replicates) and custom maskless array tiling most of ENCODE with 36mer oligonucleotides end-to-end (2 biological replicates). The chromatin-immunoprecipitation protocol is the same for all samples, however the labelling and hybridization protocols differ between Nimblegen and custom maskless arrays. Keywords = Transcription Factor Binding, STAT1, ChIP-chip, Human, Genome Tiling Arrays Keywords: other

2005-05-27 | GSE2714 | GEO

Genes specific to cowpea: cowpea vs adzuki bean

Project description:Comparative hybridization analysis Microarray-based genomic hybridization was used here as a high-throughput analog to traditional southern hybridization, which is the classical standard method for detecting specific DNA fragments in a genome.

2018-04-25 | GSE113644 | GEO

Homo sapiens

Project description:Across array comparative genomic hybridization

| PRJNA101809 | ENA

Oral dysplasias and oral squamous cell carcinoma

Project description:Analysis of DNA from 94 oral lesions by whole genome tiling-path array comparative genomic hybridization. Keywords: array comparative genomic hybridization

2008-12-31 | GSE9193 | GEO

Tiling-set aCGH data for oral dysplasias and oral squamous cell carcinomas

Project description:Analysis of DNA from 89 oral lesions by whole genome tiling-path array comparative genomic hybridization. Keywords: array comparative genomic hybridization

2009-07-01 | GSE11275 | GEO

Array CGH analysis of glioblastoma serum grown adherent cultures

Project description:We performed array comparative genomic hybridization of spheroid cultures derived from 13 glioblastomas. Keywords: comparative genomic hybridization

2010-02-13 | GSE14819 | GEO

Homo sapiens

Project description:Cross-Platform Array Comparative Genomic Hybridization (array CGH) Meta-Analysis

| PRJNA96691 | ENA

aCGH Detects Copy Number Variation with Similar Resolution to PacBio Sequencing Approaches

Project description:This study examines genomic copy-number variation between two African cichlid species through array comparative genomic hybridization. Probe level hybridization ratios were compared to copy number variation identified in Illumina and Pacific Biosciences genome assemblies from both species. Array comparative genomic hybridization was performed with 3 samples (1 replicate array setup) of genomic DNA from Maylandia zebra vs. Orechromis niloticus XX clone genomic DNA from University of Stirling clonal lines.

2019-12-14 | GSE141976 | GEO

Homo sapiens

Project description:Array-Based Comparative Genome Hybridization in Clinical Genetics

| PRJNA95545 | ENA