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Sample GSM244898 Query DataSets for GSM244898
Status Public on Nov 26, 2007
Title 38_CON.M1W4.CEL, Experimental replicate 4
Sample type RNA
 
Source name Soybean cultivar CONRAD - Mock Inoculated (Inoculated with water + agar): 24 hours post inoculation
Organism Glycine max
Characteristics cultivar - CONRAD
Tissue/Cell Type: Soybean root/hypocotyls - P.sojae mycelium from minimal medium
total Soybean RNA Plus 0.03125 % P.sojae RNA added
Treatment protocol Inoculation assays were performed using the slant board technique (Olah and Schmitthenner, 1985).[ Briefly, 7-day-old soybean seedlings were thoroughly rinsed under tap water and placed in an inoculation tray (10 plants per tray, 3 trays per inoculation replication). The plants were wounded at 2 cm below the beginning of the root zone by scraping the epidermis with a scalpel and then inoculated with a mycelial slurry from a 7-day-old culture or agar alone. Samples of root tissues were collected at 3 and 5 days post inoculation (dpi) from 7.5 mm below and above the lesion margin from each seedling with characteristic lesions. For the mock-inoculated plants, tissue sections were taken 7.5 mm below and above the position corresponding to the average lesion length measured from the inoculated samples. The lesion length (mm) from the inoculation point up to the edge of the lesion margin was also measured 3 and 5 dpi. For each experimental replication, 2 replicates of 30 seedlings per condition were inoculated and harvested separately. All the plants for an experiment were grown in the same environmental growth chamber (Chagrin Falls, Ohio; Model M-48 with TC2 microcontroller unit) with day and night temperatures settings of 27C and 21C and relative humidity averaging 75 to 90%.
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 The RNA samples isolated from each of the two inoculation replications were pooled in equal amounts before subjecting to microarray assay. RNA samples from mock inoculated tissue contain 0.03125-4% spike-in RNA from Phytophthora sojae mycellium grown in liquid sucrose-salts medium , depending upon resistance level and sampling time. 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 CONRAD - Mock inoculated; 24 hrs; ExpRep4
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 Nov 26, 2007
Last update date Aug 14, 2011
Contact name sucheta Tripathy
E-mail(s) [email protected]
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)
GSE9687 Expression patterns in time and space during P.sojae infection of soybean cultivars differing in quantitative resistance

Data table header descriptions
ID_REF Gene IDs
VALUE RMA processed value

Data table
ID_REF VALUE
AFFX-BioB-3_at 6.26040379046447
AFFX-BioB-5_at 6.61580937949771
AFFX-BioB-M_at 6.50997529707683
AFFX-BioC-3_at 7.63982154451602
AFFX-BioC-5_at 7.93841678171125
AFFX-BioDn-3_at 10.4313594571894
AFFX-BioDn-5_at 9.3130994465787
AFFX-CreX-3_at 12.5249285011412
AFFX-CreX-5_at 12.2156074425708
AFFX-DapX-3_at 2.88556101185764
AFFX-DapX-5_at 2.93919165816213
AFFX-DapX-M_at 2.80020425895598
AFFX-Gm_18SrRNA_at 7.63845398019713
AFFX-Gm_Actin_3_at 9.71903233595905
AFFX-Gm_Actin_5_at 4.86831506245238
AFFX-Gm_Actin_M_at 8.81939859025213
AFFX-Gm_GlutTrans_3_r_at 9.45221096535557
AFFX-Gm_GlutTrans_5_s_at 9.29434716310772
AFFX-Gm_GlutTrans_M_at 8.74781595736409
AFFX-Gm_P450_3_s_at 12.9895609527454

Total number of rows: 61170

Table truncated, full table size 2240 Kbytes.




Supplementary file Size Download File type/resource
GSM244898.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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