NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM294007 Query DataSets for GSM294007
Status Public on May 30, 2008
Title 5_3095.2F.R9F1U, Experimental replicate 2
Sample type RNA
 
Source name Soybean cultivar VP RIL 9 - susceptible line - RNA taken from upper side of inoculation - inoculated with pathogen P. sojae: 1 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 3.545462
Gma.1.1.S1_at 2.512231
Gma.10.1.S1_at 2.400832
Gma.100.1.A1_at 4.670935
Gma.10004.1.S1_at 8.566569
Gma.10005.1.S1_at 6.919073
Gma.1001.1.A1_at 7.465931
Gma.10013.1.S1_at 7.560176
Gma.10015.1.S1_at 9.975128
Gma.10016.1.S1_at 8.313022
Gma.1002.1.A1_at 2.719054
Gma.1002.2.S1_at 2.124802
Gma.10024.1.S1_at 2.130467
Gma.10026.1.S1_at 8.557291
Gma.10027.1.S1_at 2.442466
Gma.10029.1.S1_at 7.701132
Gma.1003.1.S1_at 8.891389
Gma.10031.1.S1_at 8.956510
Gma.10032.1.S1_at 2.658130
Gma.10033.1.A1_at 4.347133

Total number of rows: 37593

Table truncated, full table size 1081 Kbytes.




Supplementary file Size Download File type/resource
GSM294007.CEL.gz 4.5 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap