|
| Status |
Public on Sep 30, 2011 |
| Title |
2008 ripe grapes, EL36, biological replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
ripe grapes
|
| Organism |
Vitis vinifera |
| Characteristics |
developmental stage: EL36
variety: Trincadeira
tissue: pulp and skin
|
| Treatment protocol |
Grapes corresponding to the developmental stages of EL 32, 34, 35, 36, and 38 (E-L refers to the modified Eichhorn and Lorenz developmental scale) were immediately frozen in liquid nitrogen and transported to the lab in dry ice. Grapes were grinded in liquid nitrogen and seeds removed with a pincet
|
| Growth protocol |
Grapevine plants were growing at Plansel´s vines located in Montemor-o-Novo (Southern Portugal).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated essentially as described by Rerie et al. (1991, Mol Gen Genet) using phenol/ chloroform with modifications
|
| Label |
biotin
|
| Label protocol |
cDNA was synthesized from 4 µg of total RNA using One-cycle target labeling and control reagents (Affymetrix, Santa Clara, CA) to produce biotin labeled cRNA which was then fragmented at 94ºC for 35 min into 35-200 bases in length
|
| |
|
| Hybridization protocol |
Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino) ethanesulfonic acid, 1 M NaCl, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45ºC .
|
| Scan protocol |
Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix) and scanned at 1.56 µm resolution in a GeneChip® Scanner 3000 7G System (Affymetrix).
|
| Description |
Gene expression data from skin and pulp of ripe grapes
|
| Data processing |
Robust Muti-array Analysis (RMA) algorithm was used for background correction, normalization and expression levels summarization. Next, differential expression analysis was performed with the Bayes t-statistics from the linear models for Microarray data (limma), included in the affylmGUI package. P-values were corrected for multiple-testing using the Benjamini-Hochberg’s method
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| |
|
| Submission date |
Apr 21, 2011 |
| Last update date |
Sep 30, 2011 |
| Contact name |
Ana Margarida Fortes |
| E-mail(s) |
[email protected]
|
| Phone |
+351 21 7500382
|
| Organization name |
BIOFIG_FCUL
|
| Department |
Plant Biology
|
| Lab |
Biotechnology and Plant Molecular Biology
|
| Street address |
Campus da FCUL
|
| City |
Lisboa |
| ZIP/Postal code |
1749-016 |
| Country |
Portugal |
| |
|
| Platform ID |
GPL11004 |
| Series (1) |
| GSE28779 |
Transcript and metabolite analysis in Trincadeira cultivar reveals novel information regarding the dynamics of grape ripening |
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