Transcriptomics

Dataset Information

33

Comparison of gene expression profile of gilthead seabream mineralization-induced VSa16 cells against controls


ABSTRACT: In the present study, the Agilent-016251 Sparus aurata oligo microarray platform (GEO accession: GPL6467) was used to compare expression profiles of mineralization-induced VSa16 cell cultures against untreated ones. ECM mineralization was induced for 4 weeks by supplementing medium with 50 µg/ml of L-ascorbic acid, 10 mM β glycerophosphate and 4 mM CaCl2. For each group, total RNA was extracted from three (3) independent biological replicates, each consisting of pools of cells. Data analysis demonstrated that expression profiles were strongly affected by ECM mineralization with hundreds of genes differentially expressed with relevant fold-change. In this study, we analyzed six (6) cell samples, three (3) collected from untreated VSa16 cell cultures and three (3) collected from mineralization-induced VSa16 cell cultures. Gene expression profiling was performed using Agilent-016251 Sparus aurata oligo microarray platform (GPL6467) (6 arrays, no replicate) 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 that was left after all the FE processing steps was ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

ORGANISM(S): Sparus aurata  

SUBMITTER: Serena Ferraresso  Luca Bargelloni   Daniel M Tiago   Leonor M Cancela   Vincent Laizé    

PROVIDER: E-GEOD-18941 | ArrayExpress| 2011-06-17

SECONDARY ACCESSION(S): GSE18941PRJNA121061

REPOSITORIES: GEO, ArrayExpress

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