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Sample GSM170928 Query DataSets for GSM170928
Status Public on Feb 22, 2007
Title V2 Control, biological rep3
Sample type RNA
Source name Glycine max uninoculated leaf (Control)
Organism Glycine max
Characteristics 5601T unknown reaction to Asian soybean rust
Leaf samples collected 72 hours after inoculation from V2 growth stage)
Treatment protocol Under surface of the Asian soybean rust infected leaves were gently robbed on the upper surface of V2 stage plant leaves).
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 164.1052
AFFX-BioB-5_at 143.01549
AFFX-BioB-M_at 246.77411
AFFX-BioC-3_at 573.1024
AFFX-BioC-5_at 494.46225
AFFX-BioDn-3_at 2929.823
AFFX-BioDn-5_at 1805.7832
AFFX-CreX-3_at 18577.4
AFFX-CreX-5_at 14829.938
AFFX-DapX-3_at 5.0041595
AFFX-DapX-5_at 5.0758643
AFFX-DapX-M_at 5.2129555
AFFX-Gm_18SrRNA_at 48.849422
AFFX-Gm_Actin_3_at 1534.3198
AFFX-Gm_Actin_5_at 9.116192
AFFX-Gm_Actin_M_at 408.2827
AFFX-Gm_GlutTrans_3_r_at 8641.708
AFFX-Gm_GlutTrans_5_s_at 10252.347
AFFX-Gm_GlutTrans_M_at 2569.0864
AFFX-Gm_P450_3_s_at 9218.808

Total number of rows: 61170

Table truncated, full table size 1802 Kbytes.

Supplementary file Size Download File type/resource
GSM170928.CEL.gz 5.5 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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