|
| Status |
Public on Aug 10, 2015 |
| Title |
48h_r2 |
| Sample type |
RNA |
| |
|
| Source name |
Botrytis cinerea B0510_wild-type
|
| Organism |
Botrytis cinerea B05.10 |
| Characteristics |
genotype: wild-type
growth condition: 48h on mature grapevine berries (Marselan cultivar)
|
| Growth protocol |
The equatorial areas of berries were inoculated with B. cinerea conidia. The inoculated berries were kept in clear plastic boxes in 100% relative humidity in a growth chamber with fluorescent light tubes. Peel samples were collected at 16h, 24h, 48h. For the mycelium control, B. cinerea was cultivated on minimal media during 48h with the same light conditions that for the infected berries.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted according to the total RNA isolation protocol described by Reid et al. (2006), but with 10M rather than 8M LiCl, and resuspended in RNAse/DNAse-free water. The total RNA was then treated with a DNA-freeTM kit to remove any trace of DNA (Ambion – Applied Biosystems).
|
| Label |
Cy3
|
| Label protocol |
Synthesis of double-stranded cDNA and Cy3-labeling were done by PartnerChip (Evry, France) using the procedures established by NimbleGen (Roche) and the reagents from Invitrogen (Life technologies, France)
|
| |
|
| Hybridization protocol |
Hybridization on microarrays were done by PartnerChip (Evry, France) using the procedures established by NimbleGen (Roche) and the reagents from Invitrogen (Life technologies, France).
|
| Scan protocol |
Scanning was performed by PartnerChip (Evry, France) using NimbleScan.
|
| Description |
This sample is of wild-type Botrytis cinerea B0510, cultured on mature grapevines at 48h. It is the second of three 48h biological replicates used in this experiment, each from separate cultures.
|
| Data processing |
The raw data (.pair file) were subjected to RMA background correction (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), and quantile normalization (Bolstad et al. Bioinformatics 19(2):185), as implemented in the ANAIS website (http://anais.versailles.inra.fr/). Probe data were summarized by gene.
|
| |
|
| Submission date |
Feb 03, 2015 |
| Last update date |
Aug 10, 2015 |
| Contact name |
Adeline SIMON |
| Organization name |
INRAE
|
| Lab |
BIOGER
|
| Street address |
22 place de l'agronomie
|
| City |
Palaiseau |
| ZIP/Postal code |
91120 |
| Country |
France |
| |
|
| Platform ID |
GPL17773 |
| Series (1) |
| GSE65559 |
Analysis of the molecular dialogue between Botrytis cinerea and Vitis vinifera reveals a clear shift in defence mechanisms during berry ripening. |
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