Transcriptomics

Dataset Information

3

Technical replicates to determine array-to-array reproducibility.


ABSTRACT: Technical replicates, consisting of four independent hybridizations of the same labelled cRNA, were performed to determine array-to-array reproducibility. After normalization, correlation index between all replicates exceeded 98%. In this study, we analyzed reproducibility of Agilent-016251 Sparus aurata Oligo Microarray based on single-colour detection (Cyanine-3 only). A RNA sample, prepared mixing four different larval stages of gilthead sea bream, was labelled in according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol. The same labelled cRNA was used for four independent fragmentation reactions and then hybridized spanning all array positions of 4x44K platform. Microarrays are 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 are scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software creates a unique ID for each pair of XDR scans and saves it to both scan image files. Feature Extraction 9.5 uses 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): Sparus aurata  

SUBMITTER: Luca Bargelloni  

PROVIDER: E-GEOD-12118 | ArrayExpress | 2009-02-19

SECONDARY ACCESSION(S): GSE12118PRJNA113521

REPOSITORIES: GEO, ArrayExpress

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Publications

Development and validation of a gene expression oligo microarray for the gilthead sea bream (Sparus aurata).

Ferraresso Serena S   Vitulo Nicola N   Mininni Alba N AN   Romualdi Chiara C   Cardazzo Barbara B   Negrisolo Enrico E   Reinhardt Richard R   Canario Adelino V M AV   Patarnello Tomaso T   Bargelloni Luca L  

BMC genomics 20081203


BACKGROUND: Aquaculture represents the most sustainable alternative of seafood supply to substitute for the declining marine fisheries, but severe production bottlenecks remain to be solved. The application of genomic technologies offers much promise to rapidly increase our knowledge on biological processes in farmed species and overcome such bottlenecks. Here we present an integrated platform for mRNA expression profiling in the gilthead sea bream (Sparus aurata), a marine teleost of great impo  ...[more]

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