Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of baby rat kidney cells transformed with the non-oncogenic Ad5 E1 or oncogenic Ad12 E1 region, as well as primary untransformed BRK cells

ABSTRACT: Multiple rat microarrays were used to compare RNA transcript levels from 15,481 genes of baby rat kidney (BRK) cells transformed with the non-oncogenic Ad5 E1 or oncogenic Ad12 E1 region, as well as primary untransformed BRK cells.

ORGANISM(S): Rattus norvegicus

SUBMITTER: George Blair

PROVIDER: E-MTAB-30 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Identification of genes differentially expressed as result of adenovirus type 5- and adenovirus type 12-transformation.

Strath Janet J Georgopoulos Lindsay J LJ Kellam Paul P Blair G Eric GE

BMC genomics 20090206

<h4>Background</h4>Cells transformed by human adenoviruses (Ad) exhibit differential capacities to induce tumours in immunocompetent rodents; for example, Ad12-transformed rodent cells are oncogenic whereas Ad5-transformed cells are not. The E1A gene determines oncogenic phenotype, is a transcriptional regulator and dysregulates host cell gene expression, a key factor in both cellular transformation and oncogenesis. To reveal differences in gene expression between cells transformed with oncogeni ...[more]

PMID: 19200380

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Project description:An NF-κB target gene array (Panomics, Inc., Redwood City, CA) was performed to profile the PAO1-dependent expression pattern of 111 NF-kB-regulated genes in primary human airway epithelial cells (HAECs). A small scale microarray was carried out using NF-κB target gene array kit (Panomics, Inc., Redwood City, CA). A long sense-strand oligonucleotide for each of the 111 human genes that have been previously shown to be regulated by NF-KB signaling pathway was spotted in duplicate on the nitrocellulose membrane. Biotinylated DNA was spotted along the right and bottom sides of the array membrane as control. The arrays were performed according to the manufacturer’s instructions. In brief, HAECs were stimulated for 18 hours with the heat-killed bacteria PAO1 (multiplicity of infection: 100:1). Control experiment used PBS instead of bacteria. mRNA of HAECs was isolated using biotin-labeled oligo(dT)20 and streptavidin-conjugated magnetic particles (Roche, Germany). 500 ng mRNA was used to prepare biotin-labeled cDNA probes through incorporation of biotin-dUTP into cDNA via reverse transcription reactions. Each biotin-labeled cDNA probe was hybridized to an array membrane at 42°C overnight in a hybridization incubator (Fisher Scientific, Pittsburgh, PA). The membrane was washed and subjected to further incubations with blocking buffer and subsequent streptavidin-conjugated HRP. The membrane was developed through chemiluminescence reactions and detected immediately by 1 min exposure to Hyperfilm ECL X-ray films (Amersham, Piscataway, NJ). The dots on the array were quantified through densitometric analysis using GeneTools (Syngene, Frederick, MD) and the value of each dot was determined as D = (signal value – background value)/mean value of biotinylated DNA dots. Ratio (Dbacteria: Dcontrol) was used to determine the effect of bacteria stimulation on the gene regulation. Ratio>1 indicated an up-regulation of the gene. The experiments include two samples, one PBS control sample and one PAO1-stimulated sample.

Dataset Information

Transcription profiling of baby rat kidney cells transformed with the non-oncogenic Ad5 E1 or oncogenic Ad12 E1 region, as well as primary untransformed BRK cells

Publications

Identification of genes differentially expressed as result of adenovirus type 5- and adenovirus type 12-transformation.

Similar Datasets

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