Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of adult male whole MutaMouse lung with its immortalized 100% confluent epithelial lung cell line counterpart (Agilent oligo array)

ABSTRACT: Biological comparison of gene expression profiles of adult male whole MutaMouse lung with its immortalized 100% confluent epithelial lung cell line counterpart. White, P.A.,et al. 2003. Development and characterization of an epithelial cell line from MutaMouse lung. Environ Mol Mutagen 42,3 pgs 166-184

ORGANISM(S): Mus musculus

SUBMITTER: Neena Parbhakar

PROVIDER: E-MEXP-112 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Comprehensive comparison of six microarray technologies.

Yauk Carole L CL Berndt M Lynn ML Williams Andrew A Douglas George R GR

Nucleic acids research 20040827 15

Microarray technology is extensively used in biological research. The applied technologies vary greatly between laboratories, and outstanding questions remain regarding the degree of correlation among approaches. Recently, there has been a drive toward ensuring high-quality microarray data by the implementation of MIAME (Minimal Information About a Microarray Experiment) guidelines and an emphasis on ensuring public-availability to all datasets. However, despite its current widespread use and av ...[more]

PMID: 15333675

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Project description:In this study, we employ high-density oligonucleotide microarrays to characterize the MutaMouse FE1 cell line at various stages of cell growth, in primary MutaMouse lung epithelial cell cultures, and in whole lung. Global transcriptional analysis and real-time RT-PCR was applied to (1) further define the cellular origin of the FE1 cell line and its responses under different culture conditions (media and substratum), (2) provide insight into the transcriptional differences in cellular processes between FE1 cultures compared to whole lung tissues, more specifically in toxicological response, and (3) preliminarily examine FE1 culture response to exposure of benzo(a)pyrene compared to whole animals. Total RNA samples from 3 cell culture types (50% FE1, %100 FE1, and Primary lung) or MutaMouse lung were labeled with Cyanine 5-CTP, and universal reference total RNA (Stratagene, CA, USA) was labeled with Cyanine 3-CTP (Perkin Elmer Life Sciences, Woodbridge, ON, Canada) using Agilent linear Amplification kits (Agilent Tech. Inc. Mississauga, ON, Canada) following the manufacturer's instruction. Briefly, double-stranded cDNA was synthesized using MMLV-RT with T7 promoter primer, starting with 5 ug total RNA. Cyanine-labeled cRNA targets were in vitro transcribed using T7 RNA polymerase. The synthesized cRNA was precipitated by LiCl and fragmented at 60 degrees C for 30 min with fragmentation solution. Cy5- sample cRNA and Cy3- reference cRNA were hybridized to Agilent mouse development microarrays (containing ~20,000 unique 60 mer oligonucleotides; Agilent Tech. Inc. Mississauga, ON, Canada) at 60 degrees C overnight with Agilent hybridization solution and washed according to manufacturer's instruction. Arrays were scanned on a VersArray ChipReader (BioRad Laboratories Ltd., Waterloo, Ontario, Canada), and data were acquired with ImaGene 5.5 (BioDiscovery, Inc. CA, USA). Present calls were determined as signals that were greater than the mean plus three times the standard deviation of the average of the negative control spots.

Dataset Information

Transcription profiling of adult male whole MutaMouse lung with its immortalized 100% confluent epithelial lung cell line counterpart (Agilent oligo array)

Publications

Comprehensive comparison of six microarray technologies.

Similar Datasets

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