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Expression data from the seed coats of black (iRT) and brown (irT) soybean variant for alleles of the R locus
Nikola Kovinich, Agriculture and Agri-Food Canada, Department of Bioprocesses, Ottawa, Canada (kovinichn@agr.gc.ca)
Experiment design (6 hybridizations)
genotype
•Black Seed Coat(iRT) •Brown Seed Coat(irT)

This experiment has been imported by PLEXdb from NCBI GEO (GSE26208)

Series_summary:
The seed coat of black (iRT) soybean with the do...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Expression data from the seed coats of black (iRT) and brown (irT) soybean variant for alleles of the R locus
Accession No: GM43
Microarray: Soybean
Visibility: public
Experiment Type:
Experiment Factor(s):
genotype
•Black Seed Coat(iRT)   •Brown Seed Coat(irT)
Quality Control: biological replicates
Treatment summary:
 genotype  # replicates
 Black Seed Coat(iRT)  3
 Brown Seed Coat(irT)  3
Total hybridizations: 6
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE26208)

Series_summary:
The seed coat of black (iRT) soybean with the dominant R allele begins to accumulate cyanic pigments at the transition stage of seed development (300 – 400 mg fresh seed weight), whereas the brown (irT) nearly-isogenic seed coat with the recessive r allele lacks cyanic pigments at all stages of seed development. We used microarrays to determine global gene expression differences between black (iRT) and brown (irT) soybean seed coats at the transition stage of seed development (300 – 400 mg fresh seed weight).

Series_overall_design:
To identify the complete set of gene transcripts that are differentially expressed between the seed coats of black (iRT) and brown (irT) Clark isolines, seed coats were dissected at the transition stage of seed development (300 – 400 mg fresh seed weight) for microarray analysis using the Affymetrix Soybean GeneChip. To ensure seed coats were of the same stage of development, the days post anthesis, pod length, pod color, embryo morphology, and transcript levels of the developmental marker gene Gm-r1083-1191, a putative cutin biosynthesis gene, and DFR1 were ensured to be equivalent between black (iRT) and brown (irT) isolines.
Publication: 'Combined analysis of transcriptome and metabolite data reveals extensive differences between black and brown nearly-isogenic soybean (Glycine max) seed coats enabling the identification of pigment isogenes.', Kovinich N, Saleem A, Arnason JT, Miki B.
BMC Genomics 2011 Jul 29;12:381.
pubmed: 21801362
Created: 2011-09-22 09:12:22
Last Update: 2011-09-22 11:51:44
Released: 2011-09-22
GEO Accession GSE26208
Submitter: PLEXdb Curator
Name: Nikola Kovinich
Institution: Agriculture and Agri-Food Canada, Department of Bioprocesses, Ottawa, Canada
Head of Laboratory: Nikola Kovinich
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