|
| Status |
Public on Jan 03, 2013 |
| Title |
Control_T4_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Sparus aurata pre-osteoblast cell line
|
| Organism |
Sparus aurata |
| Characteristics |
cell line: VSa16 pre-osteoblast cell line
transfection: control
time: T4 (4 weeks of cell confluency)
|
| Treatment protocol |
F2 VSa16 cells were transfected with FHL2 gene as follows: coding sequence of gilthead seabream FHL2 cDNA was inserted into the expression vector pcDNA3.1 and FLAG epitope was added at its 5’ end. Construction was delivered into gilthead seabream pre-osteoblast VSa16 cells and then transfected cells were cultured for 3 weeks in medium supplemented with 300 µg/ml of geneticin. Clones resistant to antibiotic were selected, transferred to new plates and further cultured.
|
| Growth protocol |
VSa16 cells were cultured in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 2 mM L-glutamine, antibiotics and antimycotics.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extracted according to Ambion TRI Reagent® protocol
|
| Label |
Cy3
|
| Label protocol |
Amplified and labeled with Cy3 according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol
|
| |
|
| Hybridization protocol |
Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol. Gene expression profiling was performed using the Agilent-016251 Sparus aurata Oligo Microarray platform based on single-colour detection (Cyanine-3 only).
|
| Scan protocol |
Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%).
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) 9.6 used XDR ID to link the pairs of scans together automatically when extracting data.
|
| Description |
WT_T4_1
Control (WT) VSa16 cells collected at T4_rep1
|
| Data processing |
Data processed with FeatureExtraction v9.5 and Cyclic lowess normalized using R2.6.1 statistical software.
|
| |
|
| Submission date |
Sep 30, 2011 |
| Last update date |
Jan 04, 2013 |
| Contact name |
Serena Ferraresso |
| E-mail(s) |
serena.ferraresso@unipd.it
|
| Phone |
+39 049 8272506
|
| Organization name |
University of Padova
|
| Department |
Dept of Comparative Biomedicine and Food Science
|
| Street address |
Viale dell'Università
|
| City |
Legnaro (PD) |
| State/province |
Padova |
| ZIP/Postal code |
35020 |
| Country |
Italy |
| |
|
| Platform ID |
GPL6467 |
| Series (1) |
| GSE32501 |
Overexpression of four and a half LIM domains protein 2 promotes epithelial-mesenchymal transition-like phenotype in fish pre-osteoblasts |
|
