|
| Status |
Public on Dec 31, 2020 |
| Title |
IC-cellophane-rep4 |
| Sample type |
RNA |
| |
|
| Source name |
Botrytis cinerea B05.10
|
| Organism |
Botrytis cinerea |
| Characteristics |
genotype/variation: Wild-type
growth condition: solid PDB 1/4 covered with cellophane sheets
|
| Growth protocol |
Botrytis cinerea conidia were spread onto cellophane sheets placed on PDB 1/4-agar plates and harvested after 44h of culture when infection cushions (IC) represented about 40% of the surface of the plates. For the Mycelium control (Myc), conidia were cultivated in liquid PDB medium diluted 1/4 during 44h with agitation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 4 mg of lyophilized grounded material using the RNeasy Midi kit (Qiagen), and according to the manufacturerʼs instructions. A DNase treatment (Ambion) was performed to remove traces of genomic DNA. RNA profiles were assessed using the Bioanalyzer RNA 6000 Nano kit (Agilent).
|
| Label |
Cy3
|
| Label protocol |
Synthesis of double-strand cDNA and Cy3-labelling were done following the procedures established by Nimblegen (Roche) and using reagents from Invitrogen (Life Technologies, France)
|
| |
|
| Hybridization protocol |
Hybridizations on microarrays were done using the procedures established by Nimblegen (Roche) and the reagents from Invitrogen (Life Technologies, France)
|
| Scan protocol |
Scanning was performed using Agilent scanner at 532nm optimized for Nimblegen 4-plex arrays
|
| Description |
This sample is of wild-type Botrytis cinerea B05.10, cultured for 44h on PDB medium diluted 1/4, supplemented with agar and covered with a cellophane sheet. It is the fourth of fourth Infection Cushion (IC) biological replicates used in this experiment, each from separate cultures.
|
| Data processing |
The raw data (.pair files) were subjected to RMA-background correction, quantile normalization, and gene summarization (Irizarry et al., 2003; Bolstad et al., 2003) as implemented in the ANAIS website( http://anais.versailles.inra.fr).
|
| |
|
| Submission date |
Dec 11, 2019 |
| Last update date |
Jan 01, 2021 |
| Contact name |
MATHIAS CHOQUER |
| E-mail(s) |
mathias.choquer@univ-lyon1.fr
|
| Organization name |
UNIVERSITE LYON1
|
| Lab |
Microbiologie, Adaptation et Pathogénie, UMR 5240
|
| Street address |
10, rue Raphaël Dubois
|
| City |
VILLEURBANNE |
| ZIP/Postal code |
69100 |
| Country |
France |
| |
|
| Platform ID |
GPL27896 |
| Series (1) |
| GSE141822 |
The infection cushion: a fungal weapon for plant-biomass destruction |
|
