Comment[ArrayExpressAccession]	E-GEOD-21598
MAGE-TAB Version	1.1						
Public Release Date	2015-04-29
Investigation Title	Identification of genes differentially expressed between developing seeds of different soybean varieties						
Comment[Submitted Name]	Identification of genes differentially expressed between developing seeds of different soybean varieties
Experiment Description	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 GeneChips® 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. 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.						
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl					
Person Last Name	Gibson	Lin	Gibson	Glazebrook	Katagiri	Orf	
Person First Name	Susan	Rongshuang	Susan	Jane	Fumiaki	James	
Person Mid Initials	I		I			H	
Person Email	gibso043@umn.edu						
Person Affiliation	University of Minnesota						
Person Phone	612-624-7408						
Person Address	Plant Biology, University of Minnesota, 1500 Gortner Ave, St Paul, MN, USA						
Person Roles	submitter						
Protocol Name	P-GSE21598-1	P-GSE21598-5	P-GSE21598-6	P-GSE21598-2	P-GSE21598-3	P-GSE21598-4	P-GSE21598-7
Protocol Description	The data were analyzed using GCRMA function in the GCRMA package in R environment. ID_REF =  VALUE = GCRMA log2-transformed signal intensity, probes for soybean pathogens excluded	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).	Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Soybean Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.	Developing soybean seeds were collected, put on dry ice, and then transferred to -80 C until RNA extraction.	Soybean plants were grown and maintained under regular field conditions.	Extraction of total RNA was performed using Sigma Spectrum Plant Total RNA kit according to the manufacturer's instructions.	GeneChips were scanned using GeneChip Scanner 3000 7G.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	developmental stage	genotype					
Experimental Factor Type	developmental stage	genotype					
Comment[SecondaryAccession]	GSE21598						
Comment[GEOReleaseDate]	2015-04-29						
Comment[ArrayExpressSubmissionDate]	2010-04-29						
Comment[GEOLastUpdateDate]	2015-04-30						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-21598.sdrf.txt