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Sample GSM757785 Query DataSets for GSM757785
Status Public on Mar 01, 2012
Title DK21_plus_36h_1
Sample type RNA
Source name Fusarium graminearum infected with FgV1-DK21 at 36 h
Organism Fusarium graminearum
Characteristics anamorph: Fusarium graminearum
cell type: hyphae
Treatment protocol There is no special treatment in F. graminearum.
Growth protocol Virus-free and FgV1-DK21-infected F. graminearum strains were maintained on potato dextrose agar (PDA) at 25°C with 12 h light–dark cycle. Freshly grown mycelia from PDA media plate were inoculated in 50 or 200 ml of complete media (CM) broth and incubated at 25°C for 36 hrs or 120 hrs in an orbital shaker (150 rpm). Hyphae were collected by filtering through 3MM paper, washed with distilled water, dried by blotting with paper towels and frozen at -80°C.
Extracted molecule total RNA
Extraction protocol Frozen mycelia were pulverized with mortar and pestle using liquid nitrogen for nucleic acid extraction. Total RNAs were extracted by Iso-RNA Lysis reagent (5 PRIME, Germany). Extracted total RNA was treated with DNase I (Takara, Japan) to remove genomic DNA according to instructions provided by the manufacturer. The total RNA sample were precipitated with ethanol and resuspended in DEPC-treated water finally.
Label Cy3
Label protocol Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See
Hybridization protocol Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See
Scan protocol Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See
Description This sample is of FgV1-DK21 infected Fusarium graminearum. It is the first of three virus infected biological replicates used in this experiment and is harvested at 36 hrs.
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 NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
Submission date Jul 11, 2011
Last update date Mar 01, 2012
Contact name Won Kyong Cho
Phone +82-2-880-4928
Organization name Seoul National University
Department Department of Agricultural Biotechnology and Center for Fungal Pathogenesis
Street address 5103-ho, 200-dong, Daehak-dong, Kwanak-gu
City Seoul
ZIP/Postal code 151-921
Country South Korea
Platform ID GPL13843
Series (1)
GSE30545 Genome-wide expression profiling reveals transcriptional reprogramming in Fusarium graminearum by FgV1-DK21 virus infection

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

Data table
f_gramin_000001 101.461
f_gramin_000002 139.984
f_gramin_000003 3406.03
f_gramin_000004 89.0213
f_gramin_000005 268.938
f_gramin_000006 331.088
f_gramin_000007 136.089
f_gramin_000008 78.2654
f_gramin_000009 53.149
f_gramin_000010 106.436
f_gramin_000011 96.9524
f_gramin_000012 72.764
f_gramin_000013 31.6035
f_gramin_000014 27.9128
f_gramin_000015 94.7655
f_gramin_000016 508.807
f_gramin_000017 19068.2
f_gramin_000018 61.976
f_gramin_000019 329.727
f_gramin_000020 812.065

Total number of rows: 13388

Table truncated, full table size 312 Kbytes.

Supplementary file Size Download File type/resource
GSM757785_DK21_plus_36h_1_532.pair.gz 2.1 Mb (ftp)(http) PAIR
GSM757785_DK21_plus_36h_1_532_nm_norm_RMA.pair.gz 2.2 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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