NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1538186 Query DataSets for GSM1538186
Status Public on Feb 01, 2015
Title DeltaBcLAE1_r3
Sample type RNA
 
Source name Botrytis cinerea B0510_deltaBcLAE1
Organism Botrytis cinerea
Characteristics genotype: Mutant deltaBcLAE1
Growth protocol Conidial suspensions of wild type B05.10 and mutant strains deltaBcVEL1 and deltaBcLAE1 were spread onto solid grape juice medium with cellophane overlays, and incubated for 48 h.
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 (http://www.partnerchip.fr/) using the procedures established by NimbleGen (Roche) and the reagents from Invitrogen (Life technologies, France)
 
Hybridization protocol Hybridization on microarrays were done by PartnerChip (http://www.partnerchip.fr/) using the procedures established by NimbleGen (Roche) and the reagents from Invitrogen (Life technologies, France).
Scan protocol Scanning was performed by PartnerChip (http://www.partnerchip.fr/) using NimbleScan.
Description This sample is of Botrytis cinerea B0510 mutant deltaBcLAE1, cultured onto solid grape juice medium with cellophane overlays. It is the third of four deltaBcLAE1 biological replicates used in this experiment, each from separate cultures.
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the ANAIS website (http://anais.versailles.inra.fr/).
 
Submission date Nov 05, 2014
Last update date Feb 01, 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)
GSE63021 The VELVET complex in the gray mold fungus Botrytis cinerea: impact of BcLAE1 on differentiation, secondary metabolism and virulence

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

Data table
ID_REF VALUE
AL110624 610.226355177458
AL110645 1922.96218851079
AL110650 323.348855211098
AL110654 234.956396332579
AL110689 16.5781158967732
AL110771 163.056804773402
AL110790 6995.44552184412
AL110824 62.5788962435584
AL110829 1094.34218851079
AL110841 41834.7288551775
AL110854 103.858467239818
AL110857 1254.29218851079
AL110862 13776.9455218441
AL110865 17.0272090706516
AL110879 26.5088134383827
AL110895 18.4465515141327
AL110909 723.671771844124
AL110947 158.559284066521
AL110966 20.0948154390062
AL110987 18.9490116714851

Total number of rows: 20885

Table truncated, full table size 687 Kbytes.




Supplementary file Size Download File type/resource
GSM1538186_LAE-E3.pair.gz 1.1 Mb (ftp)(http) PAIR
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap