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Sample GSM209594 Query DataSets for GSM209594
Status Public on Jan 31, 2008
Title resistant_12hours_rep3
Sample type RNA
Source name pooled soybean leaves inoculated with HW94-1 harvested 12hours
Organism Glycine max
Characteristics Glycine max PI200492 21 days old (4-5 trifolates) grown in greenhouse in sterile soil with supplemental light 16 h days
Treatment protocol Urediniospores were harvested from infected soybeans and kept under liquid nitrogen. Prior to inoculation, urediniospores were heat shocked at 40C fro 5 min and kept in a humid environment overnight. Spores were suspended in a 0.01% (v/v) Tween20/water solution and adjusted to a concentration of 250,000 spores ml-1 with a hemacytometer. Twenty-two day old soybeans (second trifoliate leaf stage) were treated with an atomizer with either of two isolates of P. pachyrhizi, HW94-1 or TW72-1, or water/tween solution at 2 ml per plant. Plants were placed in a dew chamber at 20ºC for up to 24 h, and then placed in the greenhouse set at 25ºC. Leaves were harvested from inoculated plants at 6, 12, 24, and 48 hours post inoculation and snap frozen in liquid nitrogen. 4-6 leaves were pooled for each sample
Growth protocol Glycine max (Merr.) cultivar Komata (USDA germplasm accession PI200492) was seeded, grown, and maintained in a greenhouse with supplemental lighting to achieve 16 hour days
Extracted molecule total RNA
Extraction protocol trizol/guanidium isothiocyanate extraction (Chomczynski and Sacchi, 1987), followed by lithium chloride precipitation, DNAse treatment
Label biotin
Label protocol Affymetrix one cycle labeling kit following manufacturer's instructions
Hybridization protocol 45C, 60 rpms, 16 hours
Scan protocol Affymetrix Gene Scanner 3000
Description C3-3
Data processing Only the Gma probes were used for the analysis. After removal of the non-Gma proces in the R programming environment, the resulting data set was normalized, scaled and background subtracted using RMA. We used the default options in the fitPLM fucntion in affyPLM: RMA convolution for background subtraction and quantile normalization. Data for multiple spots referring to one transcript were summarized using RMA tranformation of probe level data to gene expression level data. log2 expression values were tested for differences between Resistant and Susceptible using the moderated t statistic, and the results were filtered such that genes with a p,0.05 and and absolute fold change > 1.5 were considered significantly different.
Submission date Jul 10, 2007
Last update date Aug 14, 2011
Contact name katherine schneider
Phone 301-619-5256
Fax 301-619-2880
Organization name USDA
Department FDWSRU
Lab Frederick
Street address 1301 Ditto Ave
City Ft. Detrick
State/province MD
ZIP/Postal code 21702
Country USA
Platform ID GPL4592
Series (1)
GSE8432 Expression survey of Rpp1 soybean line PI200492 resistant to P. pachyrhizi

Data table header descriptions
VALUE Normalized log2 RMA

Data table
AFFX-BioB-3_at 7.946969
AFFX-BioB-5_at 8.241624
AFFX-BioB-M_at 8.123526
AFFX-BioC-3_at 9.069123
AFFX-BioC-5_at 9.22948
AFFX-BioDn-3_at 11.233457
AFFX-BioDn-5_at 10.638527
AFFX-CreX-3_at 13.031523
AFFX-CreX-5_at 12.733645
AFFX-DapX-3_at 10.227314
AFFX-DapX-5_at 8.818917
AFFX-DapX-M_at 9.763561
AFFX-Gm_18SrRNA_at 7.858384
AFFX-Gm_Actin_3_at 9.69572
AFFX-Gm_Actin_5_at 3.996941
AFFX-Gm_Actin_M_at 8.248922
AFFX-Gm_GlutTrans_3_r_at 11.090598
AFFX-Gm_GlutTrans_5_s_at 11.606033
AFFX-Gm_GlutTrans_M_at 9.827344
AFFX-Gm_P450_3_s_at 11.931781

Total number of rows: 37744

Table truncated, full table size 1081 Kbytes.

Supplementary file Size Download File type/resource
GSM209594.CEL.gz 4.3 Mb (ftp)(http) CEL
GSM209594.CHP.gz 334.7 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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