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Sample GSM171693 Query DataSets for GSM171693
Status Public on Nov 09, 2007
Title 31_Z.I.M.5, Experimental replicate Z
Sample type RNA
 
Source name Soybean cultivar SLOAN - Mock Inoculated (Inoculated with water + agar): 120 hours post inoculation
Organisms Glycine max; Phytophthora sojae
Characteristics cultivar - SLOAN
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
E-mail(s) sutripa@vbi.vt.edu
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
ID_REF Gene IDs
VALUE RMA processed value

Data table
ID_REF VALUE
AFFX-BioB-3_at 6.29558214683885
AFFX-BioB-5_at 6.68126447521626
AFFX-BioB-M_at 6.80203204946905
AFFX-BioC-3_at 8.07743782426131
AFFX-BioC-5_at 8.23519380009631
AFFX-BioDn-3_at 10.8127506112454
AFFX-BioDn-5_at 9.608312271097
AFFX-CreX-3_at 12.7099730616442
AFFX-CreX-5_at 12.3601154884368
AFFX-DapX-3_at 2.74273145461324
AFFX-DapX-5_at 2.6123970064624
AFFX-DapX-M_at 2.65640451968665
AFFX-Gm_18SrRNA_at 7.54969918895283
AFFX-Gm_Actin_3_at 9.6030553076077
AFFX-Gm_Actin_5_at 4.54114409147531
AFFX-Gm_Actin_M_at 8.60359947616412
AFFX-Gm_GlutTrans_3_r_at 7.332423032856
AFFX-Gm_GlutTrans_5_s_at 9.78607722738743
AFFX-Gm_GlutTrans_M_at 6.37023204172598
AFFX-Gm_P450_3_s_at 9.9627263602898

Total number of rows: 61170

Table truncated, full table size 2241 Kbytes.




Supplementary file Size Download File type/resource
GSM171693.CEL.gz 7.9 Mb (ftp)(http) CEL
GSM171693.CHP.gz 330.0 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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