Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of flounders collected from sites of different pollution status in Northern Europe

ABSTRACT: We used the GENIPOL 12,700 clone Platichthys flesus cDNA microarray to determine and characterize gene expression profiles of environmentally sampled flounders from sites of different pollution status in Northern Europe. We then used multivariate variable selection coupled with a statistical modeling procedure to predict sampling site based on gene expression profiles.

ORGANISM(S): Platichthys flesus

SUBMITTER: Tim Williams

PROVIDER: E-MAXD-40 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Transcriptomic responses of European flounder (Platichthys flesus) to model toxicants.

Williams Tim D TD Diab Amer A Ortega Fernando F Sabine Victoria S VS Godfrey Rita E RE Falciani Francesco F Chipman J Kevin JK George Stephen G SG

Aquatic toxicology (Amsterdam, Netherlands) 20080815 2

The temporal transcriptomic responses in liver of Platichthys flesus to model environmental pollutants were studied over a 16-day time span after intraperitoneal injection with cadmium chloride (50 microg/kg in saline), 3-methylcholanthrene (25 mg/kg in olive oil), Aroclor 1254 (50 mg/kg in olive oil), tert-butyl-hydroperoxide (5 mg/kg in saline), Lindane (25mg/kg in olive oil), perfluoro-octanoic acid (100 mg/kg in olive oil) and their vehicles, olive oil (1 ml/kg) or saline (0.9%). Statistical ...[more]

PMID: 18804290

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Project description:We tested four gene enrichment and complexity reduction target preparation methods for scoring SFPs on the Affymetrix GeneChip 18k Maize Genome Array (âMaize GeneChipâ). Methylation filtration (MF), Cot filtration (CF), mRNA-derived cRNA, and amplified fragment length polymorphism (AFLP) methods were applied to three diverse maize inbred lines (B73, Mo17, and CML69) with three replications per line (36 Maize GeneChips). Due to large amounts of repetitive, mobile DNA, the maize genome requires a target preparation method that offers both a high level of gene enrichment and accurate scoring of SFPs. The objectives of this research are (i) to determine which target preparation method (CF, MF, mRNA, or AFLP) optimally enriches for gene sequences complementary to probe sequences on the Affymetrix GeneChip Maize Genome Array and (ii) to estimate SFP detection power for each target method. The AFLP technology is covered by patents, and patent applications owned by Keygene N.V. AFLP is a registered trademark of Keygene N.V. GeneChip. This work was supported in part by U.S. National Science Foundation grant DBI-0321467 and USDA-ARS. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Michael Gore. The equivalent experiment is ZM10 at PLEXdb.] Experiment Overall Design: protocol: mRNA - genotype: B73 maize inbred(3-replications) Experiment Overall Design: protocol: mRNA - genotype: Mo17 maize inbred(3-replications) Experiment Overall Design: protocol: mRNA - genotype: CML69 maize inbred(3-replications) Experiment Overall Design: protocol: Cot filtration (CF) - genotype: B73 maize inbred(3-replications) Experiment Overall Design: protocol: Cot filtration (CF) - genotype: Mo17 maize inbred(3-replications) Experiment Overall Design: protocol: Cot filtration (CF) - genotype: CML69 maize inbred(3-replications) Experiment Overall Design: protocol: Methylation filtration (MF) - genotype: B73 maize inbred(3-replications) Experiment Overall Design: protocol: Methylation filtration (MF) - genotype: Mo17 maize inbred(3-replications) Experiment Overall Design: protocol: Methylation filtration (MF) - genotype: CML69 maize inbred(3-replications) Experiment Overall Design: protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: B73 maize inbred(3-replications) Experiment Overall Design: protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: Mo17 maize inbred(3-replications) Experiment Overall Design: protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: CML69 maize inbred(3-replications)

Dataset Information

Transcription profiling of flounders collected from sites of different pollution status in Northern Europe

Publications

Transcriptomic responses of European flounder (Platichthys flesus) to model toxicants.

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