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Sample GSM617107 Query DataSets for GSM617107
Status Public on Jan 26, 2011
Title PH1_untreated_rep2
Sample type RNA
Source name PH1_complete medium_non-treated control
Organism Fusarium graminearum
Characteristics strain: PH1 (syn. NRRL31084)
Growth protocol 106 conidia were inoculated into 300 ml flasks each containing 100 ml complete medium (Leslie & Summerell, The Fusarium Laboratory Manual, Blackwell Publishing) and cultivated at 23°C with shaking at 150 rpm.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from mycelia grown in vitro with the Qiagen RNeasy Plant Mini Kit following the manufacturer’s protocol. The optional on-column DNase digestion step was performed using RNase-free DNase (Qiagen).
Label Cy3
Label protocol For sample preparation and array processing the Agilent protocol “One-color microarray-based gene expression analysis (Quick Amp Labelling)” was used (, the recommended volume of control RNAs (Agilent One-Color RNA Spike-In Kit) was added to 200 ng of total RNA. Thereafter, cyanine 3´- labelled cRNA was produced, using the Agilent Quick Amp Kit (one-color) according to the manufacturer’s protocol. Labelled cRNA was purified with the RNeasy mini kit (Qiagen). Yield and Cy3 incorporation rates were analyzed using a NanoDrop ND-1000 UV-VIS spectrophotometer. In addition, size distribution of cRNAs was assessed by a BioAnalyzer 2100.
Hybridization protocol For hybridizations, 600 ng of Cy3-labelled cRNA was used. Hybridization was set up in an Agilent Microarray Hybridization Chamber (G2534A) and incubated in an Agilent Hybridization Oven (G2545A) at 65°C and 10 rpm for 17 h. Thereafter, suggested washing steps were performed.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 8x15K array slides (scan resolution: 5 µm resolution).
Description Gene expression in untreated control culture
Data processing The microarray scan data were analyzed by Agilent's Feature Extraction software_v10.5 obtaining background subtracted and spatially detrended signal intensities. These 'gProcessedSignal' data were converted to gene signals by a median polish algorithm as implemented in the RMA algorithm. Gene signals were normalized between experiments by quantile normalization.
Submission date Nov 03, 2010
Last update date Jan 26, 2011
Contact name Rayko Becher
Organization name Martin-Luther-University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences
Department Department of Phytopathology and Plant Protection
Street address Betty-Heimann-Str. 3
City Halle/Saale
ZIP/Postal code 06120
Country Germany
Platform ID GPL11158
Series (1)
GSE25114 Genome-wide expression profiling of Fusarium graminearum in response to azole fungicide treatment

Data table header descriptions
VALUE Normalized gene signals

Data table
FGSG_00001 51.75
FGSG_00002 152.82
FGSG_00003 24.22
FGSG_00004 30.85
FGSG_00005 46.22
FGSG_00006 18.98
FGSG_00007 16.07
FGSG_00009 154.97
FGSG_00010 9.43
FGSG_00011 216.76
FGSG_00012 26.63
FGSG_00013 92.82
FGSG_00014 131.47
FGSG_00015 112.99
FGSG_00016 33.30
FGSG_00017 53.27
FGSG_00018 4578.55
FGSG_00019 17.95
FGSG_00020 134.93
FGSG_00021 269.23

Total number of rows: 13330

Table truncated, full table size 238 Kbytes.

Supplementary file Size Download File type/resource
GSM617107.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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