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ABSTRACT: Ruditapes philippinarum sequencing

PROVIDER: PRJNA1025125 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26322316_1.fastq.gz	Fastqsanger.gz
	SRR26322316_2.fastq.gz	Fastqsanger.gz
	SRR26322317_1.fastq.gz	Fastqsanger.gz
	SRR26322317_2.fastq.gz	Fastqsanger.gz
	SRR26322318_1.fastq.gz	Fastqsanger.gz

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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.

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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.

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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.

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

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Gene expression profile analysis of Manila clam (Ruditapes philippinarum) hemocytes after a Vibrio alginolyticus challenge using an immune-enriched oligo-microarray

Project description:The Manila clam (Ruditapes philippinarum) is a cultured bivalve species with high worldwide commercial importance. Nevertheless, diseases can cause high economical losses. For this reason, the study of immune genes in bivalve mollusks has increased in the last years. The present work describes the construction of the first R. philippinarum microarray containing immune-related hemocyte sequences and its application for the study of the gene transcription profiles of hemocytes from clams challenged with Vibrio alginolyticus through a time course.

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