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Series GSE11611 Query DataSets for GSE11611
Status Public on May 30, 2008
Title Combined gene expression and QTL analysis of soybean quantitative resistance to Phytophthora sojae
Organism Glycine max
Experiment type Expression profiling by array
Summary To identify soybean genes and QTLs associated with quantitative resistance to infection by the oomycete pathogen Phytophthora sojae, we conducted a very large-scale microarray experiment using 2522 Affymetrix GeneChips. The experiment involved assaying a total of 298 soybean recombinant inbred lines together with internal checks.
Overall design A total of 298 soybean recombinant inbred lines (F12 RILs, labeled from R001 to R317) derived from a G. max (V71-370) and G. soja (PI407162) cross were assayed with two experimental replicates. 295 out of the 298 RILs were assayed in experimental replicate I, with the plants organized into 16 blocks, while in experimental replicate II 288 RILs were assayed in 13 blocks. Three soybean genotypes (V71-370, Sloan and VPRIL9) were included within each block as internal controls. Replicates of each set of the three controls, incubated in the same growth chamber, were harvested at three different times (approximately 9 am, 10:30 am, and 12 pm). A P. sojae isolate, PT2004C2.S1, which is virulent to the soybean lines carrying Rps1a, Rps1b, Rps1k, Rps2, Rps3a, Rps3c, Rps4, Rps5, Rps6, or Rps7, was used in this study. For each soybean line, approximately 30 seedlings were inoculated on the roots with P. sojae and after 5 days, 7.5 mm root segments were collected from immediately above and below the upper margin of the visible lesion (referred to as the "Upper" and "Lower" infection courts). From approximately 20 mock-inoculated plants, 15 mm root segments ("Mock") were collected from positions on the roots matching the lesions on the pathogen-inoculated plants.
Citation(s) 19171053
Submission date May 29, 2008
Last update date Nov 22, 2016
Contact name sucheta Tripathy
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
Platforms (1)
GPL4592 [Soybean] Affymetrix Soybean Genome Array
Samples (2522)
GSM292158 10_C010.1A.R9A2P, Experimental replicate 1
GSM292159 12-1010.1A.R006P, Experimental replicate 1
GSM292160 13-1013.1A.R008L, Experimental replicate 1
BioProject PRJNA106239

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE11611_RAW.tar 11.3 Gb (http)(custom) TAR (of CEL)
GSE11611_part1.tar.gz 1.8 Gb (ftp)(http) TAR
GSE11611_part2.tar.gz 1.8 Gb (ftp)(http) TAR
GSE11611_part3.tar.gz 1.8 Gb (ftp)(http) TAR
GSE11611_part4.tar.gz 1.8 Gb (ftp)(http) TAR
GSE11611_part5.tar.gz 1.8 Gb (ftp)(http) TAR
GSE11611_part6.tar.gz 1.8 Gb (ftp)(http) TAR
GSE11611_part7.tar.gz 569.4 Mb (ftp)(http) TAR
Processed data included within Sample table

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