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Sample GSM171632 Query DataSets for GSM171632
Status Public on Nov 09, 2007
Title 18_W.E.I.3, Experimental replicate W
Sample type RNA
Source name Soybean cultivar OX20-8 - pathogen(P.sojae) Inoculated: 72 hours post inoculation
Organisms Glycine max; Phytophthora sojae
Characteristics cultivar - OX20-8
Tissue/Cell Type: Soybean root/hypocotyls - P.sojae mycelium from minimal medium
total Soybean RNA
Treatment protocol Soybean plants were grown in growth chambers and transferred to trays prior to inoculation. There were 3 trays for each treatment type having 10 plants each. P.sojae materials were inoculated onto the roots of the host plant and RNA extraction was carried out either on 3rd day or 5th day post inoculation. For mock inoculation, the plants were inoculated with pure water with agar
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 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 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 Feb 23, 2007
Last update date Jun 25, 2008
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)
GSE7124 Plant and pathogen gene expression during infection by P.sojae of 8 soybean cultivars varying in quantitative resistance

Data table header descriptions
VALUE RMA processed value

Data table
AFFX-BioB-3_at 7.92298279450895
AFFX-BioB-5_at 7.8925693137475
AFFX-BioB-M_at 7.84712753680143
AFFX-BioC-3_at 8.97538184542209
AFFX-BioC-5_at 9.30853758526181
AFFX-BioDn-3_at 11.4187615691392
AFFX-BioDn-5_at 10.4345161158490
AFFX-CreX-3_at 13.0808428390037
AFFX-CreX-5_at 12.8271557587900
AFFX-DapX-3_at 2.72103318777259
AFFX-DapX-5_at 2.49040179526978
AFFX-DapX-M_at 2.62898975747936
AFFX-Gm_18SrRNA_at 9.48433774327278
AFFX-Gm_Actin_3_at 8.50971488639999
AFFX-Gm_Actin_5_at 4.06479528576519
AFFX-Gm_Actin_M_at 7.07632830179047
AFFX-Gm_GlutTrans_3_r_at 8.73964071440333
AFFX-Gm_GlutTrans_5_s_at 9.46009417158622
AFFX-Gm_GlutTrans_M_at 8.05618577337098
AFFX-Gm_P450_3_s_at 13.4741578007027

Total number of rows: 61170

Table truncated, full table size 2241 Kbytes.

Supplementary file Size Download File type/resource
GSM171632.CEL.gz 7.4 Mb (ftp)(http) CEL
GSM171632.CHP.gz 338.8 Kb (ftp)(http) CHP
Processed data provided as supplementary file
Processed data included within Sample table

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