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Sample GSM1600087 Query DataSets for GSM1600087
Status Public on Aug 10, 2015
Title 48h_r3
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 third 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.

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
AL110624 2889.33501000295
AL110645 6866.8065484643
AL110650 679.834085894933
AL110654 484.007479354046
AL110689 46.6471870848083
AL110771 389.178939302717
AL110790 7941.41577923353
AL110824 502.464001112519
AL110829 479.512941701848
AL110841 4359.5565484643
AL110854 463.978815506171
AL110857 174.462043536568
AL110862 23884.1780869258
AL110865 39.0608860192901
AL110879 94.795174124322
AL110895 64.1854921735306
AL110909 45.2977366419721
AL110947 598.902107801137
AL110966 95.548975404887
AL110987 66.3588941649364

Total number of rows: 20885

Table truncated, full table size 686 Kbytes.




Supplementary file Size Download File type/resource
GSM1600087_48h_3.pair.gz 1.1 Mb (ftp)(http) PAIR
Processed data included within Sample table

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