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Sample GSM171666 Query DataSets for GSM171666
Status Public on Nov 09, 2007
Title 26_V.E.I.3, Experimental replicate V
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 7.35180697710064
AFFX-BioB-5_at 7.2828935353468
AFFX-BioB-M_at 7.27724757437528
AFFX-BioC-3_at 8.46539216205887
AFFX-BioC-5_at 8.79325450421548
AFFX-BioDn-3_at 10.9117726374524
AFFX-BioDn-5_at 9.86313108764874
AFFX-CreX-3_at 12.6485095876317
AFFX-CreX-5_at 12.4026167694504
AFFX-DapX-3_at 2.67774405645658
AFFX-DapX-5_at 2.61798578836589
AFFX-DapX-M_at 2.82480779291271
AFFX-Gm_18SrRNA_at 9.18882141179034
AFFX-Gm_Actin_3_at 8.43760164281891
AFFX-Gm_Actin_5_at 4.08526448108474
AFFX-Gm_Actin_M_at 6.99895122768702
AFFX-Gm_GlutTrans_3_r_at 8.95176048442627
AFFX-Gm_GlutTrans_5_s_at 8.97820259652253
AFFX-Gm_GlutTrans_M_at 8.13340885644078
AFFX-Gm_P450_3_s_at 13.5971000161724

Total number of rows: 61170

Table truncated, full table size 2241 Kbytes.

Supplementary file Size Download File type/resource
GSM171666.CEL.gz 7.6 Mb (ftp)(http) CEL
GSM171666.CHP.gz 334.2 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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