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Sample GSM170927 Query DataSets for GSM170927
Status Public on Feb 22, 2007
Title Rust Innoculated, biological rep2
Sample type RNA
Source name Glycine max rust inoculated leaf (Treatment)
Organism Glycine max
Characteristics 5601T unknown reaction to Asian soybean rust
Leaf samples collected 72 hours after inoculation from V2 growth stage)
Treatment protocol Control plants at V2 stage were not inoculated rather moved to an adjacent growth chamber with congruent growing environment).
Growth protocol Three plants per pot were maintained and growing environment consisted of 28/20 degree celsius, 14/10 photoperiod with high humidity.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Soybean Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Affymetrix 7G scanner.
Description Gene expression analysis in soybean in response to Phakopsora pachyrhizii.
Data processing The image was scanned using GCOS software and the corresponding CEL file generated. Array Assist was used to summarize the signal values using the GCRMA algorithm.
Submission date Feb 22, 2007
Last update date Feb 22, 2007
Contact name Dilip Raj Panthee
Phone (865)974 1903
Organization name University of Tennessee
Department Plant Sciences
Street address 2431 Joe Johnson Dr.
City Knoxville
State/province TN
ZIP/Postal code 37996
Country USA
Platform ID GPL4592
Series (1)
GSE7108 Gene expression analysis in soybean with respect to Pahakopsora pachyrhizii at V2 growth stage

Data table header descriptions
ID_REF Probe Set ID
VALUE GCRMA calculated Signal intensity

Data table
AFFX-BioB-3_at 317.32437
AFFX-BioB-5_at 234.7715
AFFX-BioB-M_at 376.08536
AFFX-BioC-3_at 1030.7137
AFFX-BioC-5_at 846.00006
AFFX-BioDn-3_at 5103.665
AFFX-BioDn-5_at 2616.3455
AFFX-CreX-3_at 24612.26
AFFX-CreX-5_at 19608.176
AFFX-DapX-3_at 4.8408637
AFFX-DapX-5_at 4.892082
AFFX-DapX-M_at 5.04425
AFFX-Gm_18SrRNA_at 62.334373
AFFX-Gm_Actin_3_at 5641.9453
AFFX-Gm_Actin_5_at 10.850816
AFFX-Gm_Actin_M_at 2470.6365
AFFX-Gm_GlutTrans_3_r_at 9700.126
AFFX-Gm_GlutTrans_5_s_at 4904.4814
AFFX-Gm_GlutTrans_M_at 5649.1665
AFFX-Gm_P450_3_s_at 3986.977

Total number of rows: 61170

Table truncated, full table size 1802 Kbytes.

Supplementary file Size Download File type/resource
GSM170927.CEL.gz 4.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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