Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Determining the wash solution to use

ABSTRACT: We tested a new wash solution from Agilent Keywords: Agilent microarray, pooling, Drosophila, intact adults Intact males and females for a single genotype were examined. Two independent replicates of each were compared on two slides in a dye flip.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Lauren McIntyre

PROVIDER: E-GEOD-5182 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Simpler mode of inheritance of transcriptional variation in male Drosophila melanogaster.

Wayne Marta L ML Telonis-Scott Marina M Bono Lisa M LM Harshman Larry L Kopp Artyom A Nuzhdin Sergey V SV McIntyre Lauren M LM

Proceedings of the National Academy of Sciences of the United States of America 20071114 47

Sexual selection drives faster evolution in males. The X chromosome is potentially an important target for sexual selection, because hemizygosity in males permits accumulation of alleles, causing tradeoffs in fitness between sexes. Hemizygosity of the X could cause fundamentally different modes of inheritance between the sexes, with more additive variation in males and more nonadditive variation in females. Indeed, we find that genetic variation for the transcriptome is primarily additive in mal ...[more]

PMID: 18003923

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Project description:Ataxia telangiectasia (AT) is an autosomal recessive disorder characterized by neuronal degeneration, telangiectasias, acute cancer predisposition, and hypersensitivity to ionizing radiation (IR). The gene defective in AT, ATM (for AT-mutated), encodes a protein, pATM that has been found to have IR-inducible kinase activity. Cells from individuals with AT exhibit severely attenuated cell cycle checkpoints in response to gamma radiation exposure. pATM has been hypothesized to act as part of a complex that senses DNA damage, in particular, DNA double strand breaks. We are studying the pATM-dependent gene expression responses to a dose of 1.5 Gy radiation in lymphoblastoid cell lines from multiple individuals with either wild type or mutated ATM. The gene expression analyses were performed on Agilent Human 1A Oligo chips containing approximately 16,000 60mer probes. We identified a set of genes whose gene expression changes are ATM-dependent following exposure to 1.5 Gy IR. This set of genes was tested by real time quantitative PCR analysis. The study consists of one dose group - 1.5 Gray gamma radiation. Samples were collected 6 hr following irradiation (treated) or mock irradiation (controls) for each culture. Each culture has a treated sample and a control sample. There are cultures from 6 wild-type ATM individuals and cultures from 6 individuals that are ATM-deficient, for a total of 12 cultures. Hybridizations compared RNA extracted from each individual culture's treated sample against its corresponding control sample, and were performed as dye-flip duplicates (1 replicate in each direction). Hybridizations were performed on the Human 1A Oligo Chips using low input, direct labeling at Paradigm Genetics Laboratory. Microarray scanning was performed with the Agilent G2565AA Scanner. Paradigm Standard Operating Procedures were followed for quality analysis, sample labeling, microarray hybridization and washing, scanning, image analysis and initial data analysis.

Dataset Information

Determining the wash solution to use

Publications

Simpler mode of inheritance of transcriptional variation in male Drosophila melanogaster.

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