Project description:These experiments were designed to determine the usefulness of the spurge/cassava euphorbiaceae arrays for investigating gene expression in other euphorbs. Keywords: heterologous hybridization euphorbia
Project description:These experiments were designed to determine the usefulness of the spurge/cassava euphorbiaceae arrays for investigating gene expression in other euphorbs. two color dye swap design
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.
Project description:Tumors often harbor several genetic aberrations at both RNA and DNA level. Integration of expression data with copy number changes represents a powerful strategy to investigate genes involved in tumorigenesis. Here we describe a fluorescent array-based Comparative Genomic Hybridization protocol to be used on a commercial microarray platform optimized to detect cancer-related gene expression. This method will be valuable to use a single low-density array platform monitoring gene expression and copy number assessment in parallel. Keywords: Comparative genomic hybridization, neuroblastoma
Project description:RNA mapping on Human chromosomes 21/22. This hybridization was done using RNA samples from 16 different human cell lines. The data obtained is from analysis done on Human Genome hs.NCBIv36 or hg18 (UCSC) Keywords: RNA mapping experiments
Project description:Fish and Chips: Expression Profiling in Non-traditional Model Systems Using a Cichlid Fish cDNA Microarray This series represents the 26 arrays that went into Renn et al 2004 (submitted January 16th), and one additional hybridization (GSM15240) that was not included in the publication analysis for statistical reasons. Keywords: other
Project description:Aim of this study is to test if a reference channel of a different array can be used to make array CGH more sensitive, cost effective and less labor intensive. The BT474 breast cancer cell line was compared to a mix of normal reference DNAs hybridized on different arrays and days and DNA copy number profiles were evaluated. Quality was assessed, using regular dual channel array CGH as a standard, using four quality measures; i.e. the MAD (median absolute deviation) value of chromosome 2, an amplitude of the ErbB2 gene amplification, a deletion on chromosome 9 and a deflection on chromosome 8. In addition, the use of a reference channel of a different array was tested for genomic DNA derived from formalin-fixed paraffin-embedded tumor tissue samples. This so called across array CGH (aaCGH) analysis yielded slightly higher quality chromosomal copy number profiles when using the same dye compared to analysis using two different dyes, both when exchanging fluorescent signals of hybridizations performed on different arrays and on different days. This approach avoids redundant hybridizations of the same reference material in every experiment and allows hybridization of two test samples on one array. AaCGH analysis substantially reduces cost of consumables and labor while yielding at least equivalent quality as the dual channel procedure. Keywords: array CGH data, across array CGH analysis