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Which role for genomics in environmental risk assessment? A case study in Venice Lagoon.

ABSTRACT: DNA microarray analyses of Ruditapes philippinarum sampled in Venice lagoon areas subjected to different anthropogenic impact.

ORGANISM(S): Ruditapes philippinarum

PROVIDER: GSE50062 | GEO | 2013/10/01

SECONDARY ACCESSION(S): PRJNA215903

REPOSITORIES: GEO

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Which role for genomics in environmental risk assessment? A case study in Venice Lagoon.

Project description:DNA microarray analyses of Ruditapes philippinarum sampled in Venice lagoon areas subjected to different anthropogenic impact. A comparative analysis of gene expression was conducted between Manila clam from lowly-polluted Chioggia and Colmata area and polluted Marghera site.

2013-10-01 | E-GEOD-50062 | biostudies-arrayexpress

Analyses of transcriptomic responses to heavy metal exposure in Manila clam collected in Venice lagoon areas characterized by different anthropogenic impact

Project description:A Ruditapes philippinarum microarray platform was developed to assess variations on transcritpomic response to copper exposures in Manila clam colelctted in Venice lagoon areas subjected to different anthropogenic impact

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Toxicogenomic analyses of Ruditapes philippinarum by DNA microarray: new tools for anthropogenic impact assessment on the Venice Lagoon.

2013-02-15 | GSE26985 | GEO

Toxicogenomic analyses of Ruditapes philippinarum by DNA microarray: new tools for anthropogenic impact assessment on the Venice Lagoon.

Project description:A manila clam oligo microarray platform (GPL10900) was used to profile gene expression in digestive gland of R. philippinarum sampled in four seasons in 4 different areas of Venice Lagoon. For each tissue, total RNA was extracted from four (4) independent biological replicates of digestive gland, each consisting of tissue pools of five (5) animals. In this study, we analyzed 64 samples (pools of 5 digestive gland). Gene expression profiling was performed using the Agilent-027304 Ruditapes philippinarum Oligo Microarray platform (GPL10900) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

2013-02-15 | E-GEOD-26985 | biostudies-arrayexpress

Biological replicates of Ruditapes philippinarum digestive gland pools

Project description:Four pools of digestive glands were treated as biological replicates in order to evaluate the repeatability of Ruditapes philippinarum oligo microarray platform.

2012-09-04 | GSE24050 | GEO

Biological replicates of Ruditapes philippinarum digestive gland pools

Project description:Four pools of digestive glands were treated as biological replicates in order to evaluate the repeatability of Ruditapes philippinarum oligo microarray platform. In this study, we analyzed four (4) independent pools of Ruditapes philippinarum digestive glands. Gene expression profiling was performed using the Agilent-027304 Ruditapes philippinarum Oligo Microarray platform (1 arrays) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

2012-09-04 | E-GEOD-24050 | biostudies-arrayexpress

Transcriptome analysis of Manila clam (Ruditapes philippinarum) digestive gland after exposure to different concentrations of ibuprofen.

Project description:A Ruditapes philippinarum microarray platform was developed to identify digestive gland gene expression profiles in response to 100 µg /l and 1000 µg/l ibuprofen exposure.

2013-10-01 | GSE38863 | GEO

Environmental pollution assessment using Mus spretus

Project description:We evaluated the suitability of high-throughput transcriptomics approach to monitor terrestrial ecosystems. Free-living Mus spretus from several polluted sites of Huelva (Andalusia, SW Spain) were compared with mice from Doñana Biological Reserve (“Santa Olalla” lagoon (SOL) used as negative control). As most popular bioindicators, M. spretus is poorly represented in gene databases, therefore limiting the use of genomics in ecotoxicological studies. To solve this problem, we used microarrays produced from mRNAs of M. musculus. Specifically we used the One-Color Gene Expression Platform commercialized by Agilent.

2013-12-31 | GSE33663 | GEO

xbRudPhil6

Project description:Ruditapes philippinarum

| PRJEB81439 | ENA

Ruditapes philippinarum

Project description:Toxicogenomic analyses of Ruditapes philippinarum by DNA microarray: new tools for anthropogenic impact assessment on the Venice Lagoon.

| PRJNA135933 | ENA

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