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Comparison of gene expression profile of gilthead seabream mineralization-induced VSa13 cells against controls

ABSTRACT: In the present study, the Agilent-016251 Sparus aurata oligo microarray platform (GPL6467) was used to compare expression profiles of mineralization-induced VSa13 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 VSa13 cell cultures and three (3) collected from mineralization-induced VSa13 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

PROVIDER: E-GEOD-18915 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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

Project description: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.

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Genome expression profile of early response to photobacteriosis in gilthead sea bream (Sparus aurata)

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Technical replicates to determine array-to-array reproducibility.

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Overexpression of four and a half LIM domains protein 2 promotes epithelial-mesenchymal transition-like phenotype in fish pre-osteoblasts

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Overexpression of four and a half LIM domains protein 2 promotes epithelial-mesenchymal transition-like phenotype in fish pre-osteoblasts

Project description:Four and a half LIM domains protein 2 (FHL2) is a co-regulator of gene transcription relevant for many signalling pathways and physiological processes. In this work, the role of FHL2 in cell differentiation has been investigated during in vitro mineralization using a Sparus aurata pre-osteoblast cell line (VSa16, [1]). A global microarray analysis was then performed to characterize the molecular pathways affected by FHL2 overexpression. [1] Pombinho, A.R., LaizM-CM-), V., Molha, D.M., Marques, S.M.P. and Cancela, M.L. (2004). Development of two bone-derived cell lines from the marine teleost Sparus aurata; evidence for extracellular matrix mineralization and cell-type specific expression of matrix Gla protein and osteocalcin. Cell Tissue Res. 315, 393-406. Sparus aurata oligo-DNA microarray (GPL6467) was used to compare gene expression profiles between Control (WT) and FHL2-transfected (F2) VSa16 cell lines. Gene expression profiles of both WT and F2 cells were assessed either at T0 (initial confluent cultures) or T4 (4 weeks of cell confluency). Four (4) pools of cells were taken from both WT and F2 groups at each time point and stored in RNA later at -20M-BM-0C until RNA extraction.

2013-01-03 | E-GEOD-32501 | biostudies-arrayexpress

Comparison of gene expression profile of gilthead seabream mineralization-induced VSa13 cells against controls

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

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