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Sample GSM244871 Query DataSets for GSM244871
Status Public on Nov 26, 2007
Title 31_SLO.I3U2.CEL, Experimental replicate 2
Sample type RNA
Source name Soybean cultivar SLOAN - pathogen(P.sojae) Inoculated: 72 hours post inoculation : Sample taken from the upper side of the inoculation
Organism Glycine max
Characteristics cultivar - SLOAN
Tissue/Cell Type: Soybean root/hypocotyls - P.sojae mycelium from minimal medium
total Soybean RNA
Treatment protocol Inoculation assays were performed using the slant board technique (Olah and Schmitthenner, 1985).[ Briefly, 7-day-old soybean seedlings were thoroughly rinsed under tap water and placed in an inoculation tray (10 plants per tray, 3 trays per inoculation replication). The plants were wounded at 2 cm below the beginning of the root zone by scraping the epidermis with a scalpel and then inoculated with a mycelial slurry from a 7-day-old culture or agar alone. Samples of root tissues were collected at 3 and 5 days post inoculation (dpi) from 7.5 mm below and above the lesion margin from each seedling with characteristic lesions. For the mock-inoculated plants, tissue sections were taken 7.5 mm below and above the position corresponding to the average lesion length measured from the inoculated samples. The lesion length (mm) from the inoculation point up to the edge of the lesion margin was also measured 3 and 5 dpi. For each experimental replication, 2 replicates of 30 seedlings per condition were inoculated and harvested separately. All the plants for an experiment were grown in the same environmental growth chamber (Chagrin Falls, Ohio; Model M-48 with TC2 microcontroller unit) with day and night temperatures settings of 27C and 21C and relative humidity averaging 75 to 90%.
Growth protocol Soybean plants were grown in growth chambers and later transferred to trays with clothes soaked in water
Extracted molecule total RNA
Extraction protocol QIAGEN RNeasy Kit : As recommended by manufacturer
Label biotin
Label protocol The RNA samples isolated from each of the two inoculation replications were pooled in equal amounts before subjecting to microarray assay. RNA samples from mock inoculated tissue contain 0.03125-4% spike-in RNA from Phytophthora sojae mycellium grown in liquid sucrose-salts medium , depending upon resistance level and sampling time. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA. RNA is is first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction is carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling. The biotinylated cRNA targets are then cleaned up, fragmented, and hybridized to GeneChip expression arrays(Affymetrix Technical manual - 2004)
Hybridization protocol hybridization cocktail is prepared, including the fragmented target, probe array controls, BSA, and herring sperm DNA. It is then hybridized to the probe array during a 16-hour incubation(Affymetrix technical manual - 2004)
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000
Description SLOAN - P.sojae inoculated; 72 hrs (upper); ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points
Data processing The data were analyzed with RMA suite from R package version 2.4.0. Background correction was using RMA followed by quantile normalization and data was summarized using median polish method
Submission date Nov 26, 2007
Last update date Aug 14, 2011
Contact name sucheta Tripathy
Phone 5402318138
Organization name Virginia Tech
Department Virginia Bioinformatics Institute
Lab Tyler lab
Street address 1, Washington street
City Blacksburg
State/province VA
ZIP/Postal code 24061
Country USA
Platform ID GPL4592
Series (1)
GSE9687 Expression patterns in time and space during P.sojae infection of soybean cultivars differing in quantitative resistance

Data table header descriptions
VALUE RMA processed value

Data table
AFFX-BioB-3_at 7.27728313266795
AFFX-BioB-5_at 7.28208350546383
AFFX-BioB-M_at 7.44322517093616
AFFX-BioC-3_at 8.31177375746435
AFFX-BioC-5_at 8.69427260676385
AFFX-BioDn-3_at 10.7964845653342
AFFX-BioDn-5_at 9.89682112423304
AFFX-CreX-3_at 12.9734043290841
AFFX-CreX-5_at 12.7519243052060
AFFX-DapX-3_at 2.95479054743541
AFFX-DapX-5_at 3.03229874017126
AFFX-DapX-M_at 2.80520783920398
AFFX-Gm_18SrRNA_at 11.6650051765078
AFFX-Gm_Actin_3_at 9.32099340495258
AFFX-Gm_Actin_5_at 4.58029752605463
AFFX-Gm_Actin_M_at 8.30351595893146
AFFX-Gm_GlutTrans_3_r_at 9.29788191495763
AFFX-Gm_GlutTrans_5_s_at 9.42877318403555
AFFX-Gm_GlutTrans_M_at 8.67145183944887
AFFX-Gm_P450_3_s_at 13.0075614967350

Total number of rows: 61170

Table truncated, full table size 2240 Kbytes.

Supplementary file Size Download File type/resource
GSM244871.CEL.gz 4.7 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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