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Sample GSM757790 Query DataSets for GSM757790
Status Public on Mar 01, 2012
Title DK21_minus_120h_3
Sample type RNA
 
Source name Virus free Fusarium graminearum at 120 hpi
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 www.nimblegen.com.
 
Hybridization protocol Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Description This sample is of wild-type Fusarium graminearum. It is the third of three wild-type biological replicates used in this experiment and is harvested together with virus infected samples at 120 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
E-mail(s) wonkyong@gmail.com
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
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
f_gramin_000001 61.4396
f_gramin_000002 102.683
f_gramin_000003 1952.26
f_gramin_000004 216.692
f_gramin_000005 244.988
f_gramin_000006 54.5668
f_gramin_000007 163.877
f_gramin_000008 80.5263
f_gramin_000009 65.6191
f_gramin_000010 76.2621
f_gramin_000011 74.0653
f_gramin_000012 53.4328
f_gramin_000013 50.0313
f_gramin_000014 362.339
f_gramin_000015 293.449
f_gramin_000016 430.25
f_gramin_000017 17735.7
f_gramin_000018 159.263
f_gramin_000019 341.144
f_gramin_000020 450.762

Total number of rows: 13388

Table truncated, full table size 312 Kbytes.




Supplementary file Size Download File type/resource
GSM757790_DK21_minus_120h_3_532.pair.gz 2.1 Mb (ftp)(http) PAIR
GSM757790_DK21_minus_120h_3_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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