Transcriptomics

Dataset Information

63

Biological replicates of Ruditapes philippinarum digestive gland pools


ABSTRACT: 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.

ORGANISM(S): Ruditapes philippinarum  

SUBMITTER: Massimo Milan   Milan Massimo  Bargelloni Luca 

PROVIDER: E-GEOD-24050 | ArrayExpress | 2012-09-04

SECONDARY ACCESSION(S): GSE24050PRJNA130251

REPOSITORIES: GEO, ArrayExpress

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Publications

Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring.

Milan Massimo M   Coppe Alessandro A   Reinhardt Richard R   Cancela Leonor M LM   Leite Ricardo B RB   Saavedra Carlos C   Ciofi Claudio C   Chelazzi Guido G   Patarnello Tomaso T   Bortoluzzi Stefania S   Bargelloni Luca L  

BMC genomics 20110512


BACKGROUND: The Manila clam, Ruditapes philippinarum, is one of the major aquaculture species in the world and a potential sentinel organism for monitoring the status of marine ecosystems. However, genomic resources for R. philippinarum are still extremely limited. Global analysis of gene expression profiles is increasingly used to evaluate the biological effects of various environmental stressors on aquatic animals under either artificial conditions or in the wild. Here, we report on the develo  ...[more]

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