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Sample GSM293080 Query DataSets for GSM293080
Status Public on May 30, 2008
Title 7_C033.1N.R9N3L, Experimental replicate 1
Sample type RNA
 
Source name Soybean cultivar VP RIL 9 - susceptible line - RNA taken from lower side of inoculation - inoculated with pathogen P. sojae: 3 days post inoculation
Organism Glycine max
Characteristics cultivar - VP RIL 9 - susceptible line
Tissue/Cell Type: Soybean root/hypocotyls - P.sojae mycelium from minimal medium
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. For RIL experiments the RILS had no specific time points but the checks did.
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 May 29, 2008
Last update date May 30, 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)
GSE11611 Combined gene expression and QTL analysis of soybean quantitative resistance to Phytophthora sojae

Data table header descriptions
ID_REF Gene IDs
VALUE RMA processed value

Data table
ID_REF VALUE
Gma.1.1.A1_at 3.401020
Gma.1.1.S1_at 3.325924
Gma.10.1.S1_at 4.044003
Gma.100.1.A1_at 3.653352
Gma.10004.1.S1_at 8.547594
Gma.10005.1.S1_at 6.584624
Gma.1001.1.A1_at 7.162960
Gma.10013.1.S1_at 7.489220
Gma.10015.1.S1_at 9.690797
Gma.10016.1.S1_at 8.398324
Gma.1002.1.A1_at 2.732167
Gma.1002.2.S1_at 2.180400
Gma.10024.1.S1_at 2.125522
Gma.10026.1.S1_at 8.644668
Gma.10027.1.S1_at 2.501579
Gma.10029.1.S1_at 7.272801
Gma.1003.1.S1_at 9.055820
Gma.10031.1.S1_at 9.266179
Gma.10032.1.S1_at 2.839091
Gma.10033.1.A1_at 2.681621

Total number of rows: 37593

Table truncated, full table size 1081 Kbytes.




Supplementary file Size Download File type/resource
GSM293080.CEL.gz 4.7 Mb (ftp)(http) CEL
Processed data included within Sample table
Raw data provided as supplementary file

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