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Sample GSM171611 Query DataSets for GSM171611
Status Public on Nov 09, 2007
Title 13_W.E.M.5, Experimental replicate W
Sample type RNA
Source name Soybean cultivar OX20-8 - Mock Inoculated (Inoculated with water + agar): 120 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 Plus 16 % P.sojae RNA added
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 7.10513509997422
AFFX-BioB-5_at 7.27684904802414
AFFX-BioB-M_at 7.19874790955044
AFFX-BioC-3_at 8.55702080264992
AFFX-BioC-5_at 8.70480842260165
AFFX-BioDn-3_at 11.2163708012718
AFFX-BioDn-5_at 10.0455394101405
AFFX-CreX-3_at 12.9670141729515
AFFX-CreX-5_at 12.6179395677506
AFFX-DapX-3_at 2.86624505571751
AFFX-DapX-5_at 2.57681505507312
AFFX-DapX-M_at 2.57622587754136
AFFX-Gm_18SrRNA_at 7.76391157498745
AFFX-Gm_Actin_3_at 9.61947211055088
AFFX-Gm_Actin_5_at 4.51347149439526
AFFX-Gm_Actin_M_at 8.36009261770099
AFFX-Gm_GlutTrans_3_r_at 7.1293467053518
AFFX-Gm_GlutTrans_5_s_at 9.34924103597202
AFFX-Gm_GlutTrans_M_at 6.61756479339049
AFFX-Gm_P450_3_s_at 10.378166209917

Total number of rows: 61170

Table truncated, full table size 2240 Kbytes.

Supplementary file Size Download File type/resource
GSM171611.CEL.gz 7.6 Mb (ftp)(http) CEL
GSM171611.CHP.gz 333.9 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data provided as supplementary file
Processed data included within Sample table

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