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Series GSE21598 Query DataSets for GSE21598
Status Public on Apr 29, 2015
Title Identification of differentially expressed genes between developing seeds of different soybean cultivars
Organism Glycine max
Experiment type Expression profiling by array
Summary Soybean is a rich source of protein and oil and a primary feedstock for biodiesel production. Previous research on soybean indicated that protein, oil and yield are controlled quantitatively in soybean seeds. However, genetic mechanisms controlling seed composition and yield in soybean remain unknown. We used Affymetrix Soybean GeneChipsĀ® to identify genes that are differentially expressed between developing seeds of the Minsoy and Archer soybean varieties, which differ in seed weight, yield, protein content and oil content. Some of the differentially expressed genes identified in this study may play important roles in controlling these traits.
 
Overall design The soybean plants of two soybean varieties Minsoy and Archer and two recombinant inbred lines from the cross that are similar in maturity but differ in yield were grown in St Paul, Minnesota during the summers of 2007 and 2008. In 2007, each line was planted as a single row. In 2008, a randomized complete block (RCB) design was used and each line had 3 replicates planted 1-2 weeks apart. Within each replicate, two rows per line were planted. Seeds were harvested at three developmental stages, namely, seed length = 2 mm, 3.5 mm, and 5-6 mm, which correspond approximately to soybean reproductive stages R4, R5 and early R6, respectively. In 2007 three independent samples were collected for each line and developmental stage. In 2008, two seed samples (one from each row) were collected for each line at each stage within each replicate. The pairs of seed samples were then pooled. Thus, three sets of independent tissue samples were collected for RNA extraction and hybridization on Affymetrix microarrys.
Web link http://www.ncbi.nlm.nih.gov/pubmed/?term=Identification+of+differentially+expressed+genes+between+developing+seeds+of+different+soybean+cultivars
 
Contributor(s) Lin R, Gibson SI, Glazebrook J, Katagiri F, Orf JH
Citation(s) 26697344
Submission date Apr 29, 2010
Last update date Nov 22, 2016
Contact name Susan I Gibson
E-mail(s) gibso043@umn.edu
Phone 612-624-7408
Organization name University of Minnesota
Department Plant Biology
Lab Sue Gibson Lab
Street address 1500 Gortner Ave
City St Paul
State/province MN
ZIP/Postal code 55108
Country USA
 
Platforms (1)
GPL4592 [Soybean] Affymetrix Soybean Genome Array
Samples (54)
GSM539211 Archer at Stage 1, biological rep1, in 2007
GSM539212 Archer at Stage 1, biological rep2, in 2007
GSM539213 Archer at Stage 1, biological rep3, in 2007
Relations
BioProject PRJNA127135

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
GSE21598_RAW.tar 293.1 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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