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Sample GSM209591 Query DataSets for GSM209591
Status Public on Jan 31, 2008
Title mock_0hours_rep3
Sample type RNA
Source name pooled soybean leaves mock- inoculated harvested time 0
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 C0
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 7.227349
AFFX-BioB-5_at 7.345253
AFFX-BioB-M_at 7.209109
AFFX-BioC-3_at 8.201444
AFFX-BioC-5_at 8.217887
AFFX-BioDn-3_at 10.421391
AFFX-BioDn-5_at 9.431606
AFFX-CreX-3_at 12.466423
AFFX-CreX-5_at 12.000495
AFFX-DapX-3_at 11.577295
AFFX-DapX-5_at 10.655539
AFFX-DapX-M_at 11.228054
AFFX-Gm_18SrRNA_at 7.552362
AFFX-Gm_Actin_3_at 10.058937
AFFX-Gm_Actin_5_at 4.315449
AFFX-Gm_Actin_M_at 8.071341
AFFX-Gm_GlutTrans_3_r_at 11.362684
AFFX-Gm_GlutTrans_5_s_at 11.690971
AFFX-Gm_GlutTrans_M_at 10.169632
AFFX-Gm_P450_3_s_at 9.427879

Total number of rows: 37744

Table truncated, full table size 1084 Kbytes.

Supplementary file Size Download File type/resource
GSM209591.CEL.gz 4.8 Mb (ftp)(http) CEL
GSM209591.CHP.gz 329.4 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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