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Sample GSM757782 Query DataSets for GSM757782
Status Public on Mar 01, 2012
Title DK21_minus_36h_1
Sample type RNA
Source name Fusarium graminearum virus free 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 wild-type Fusarium graminearum. It is the first of three wild-type biological replicates used in this experiment and is harvested together with virus infected samples 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 80.4876
f_gramin_000002 107.874
f_gramin_000003 3131.01
f_gramin_000004 78.9152
f_gramin_000005 244.975
f_gramin_000006 159.715
f_gramin_000007 164.149
f_gramin_000008 106.693
f_gramin_000009 72.5029
f_gramin_000010 100.974
f_gramin_000011 106.576
f_gramin_000012 67.5434
f_gramin_000013 33.0077
f_gramin_000014 28.9551
f_gramin_000015 93.2038
f_gramin_000016 401.915
f_gramin_000017 11884.9
f_gramin_000018 107.876
f_gramin_000019 5671.47
f_gramin_000020 4236.53

Total number of rows: 13388

Table truncated, full table size 312 Kbytes.

Supplementary file Size Download File type/resource
GSM757782_DK21_minus_36h_1_532.pair.gz 2.1 Mb (ftp)(http) PAIR
GSM757782_DK21_minus_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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