GEO DataSets

(Submitter supplied) Soybean nested association mapping (NAM) parent lines were compared by CGH to catalog structurally variant (e.g. deletion and duplication) regions among these genotypes. The CGH comparisons reveal reveal putative deletions and duplications among the 41 lines.

Organism:

Glycine max

Type:

Genome variation profiling by genome tiling array

Platform:

GPL18500

42 Samples

Download data: PAIR

(Submitter supplied) Transgenic soybean lines were compared to their parental lines by CGH to catalog structurally variant (e.g. deletion and duplication) regions among these genotypes. The CGH comparisons reveal reveal putative deletions and duplications among the 5 lines.

Organism:

Glycine max

Type:

Genome variation profiling by genome tiling array

Platform:

GPL18500

7 Samples

Download data: PAIR

(Submitter supplied) Soybean fast neutron (FN) mutant lines were compared by CGH to catalog structurally variant (e.g. deletion and duplication) regions compared to the parent line (M92-220). The CGH comparisons reveal reveal putative deletions and duplications among the mutant lines.

Organism:

Glycine max

Type:

Genome variation profiling by array

Platform:

GPL18500

146 Samples

Download data: PAIR

(Submitter supplied) CGH was used to compare induced structural variation among soybean fast neutron lines, developed in background M92-220.

Organism:

Glycine max

Type:

Genome variation profiling by genome tiling array

Platform:

GPL11198

11 Samples

Download data

(Submitter supplied) CGH was used to compare induced structural variation among soybean fast neutron lines, developed in background M92-220.

Organism:

Glycine max

Type:

Genome variation profiling by genome tiling array

Platform:

GPL11198

114 Samples

Download data

(Submitter supplied) CGH was used to compare structural variation among four soybean cultivars (Archer, Minsoy, Noir1 and Williams 82). Four additional hybridizations were performed with these and other accessions (Kingwa, Williams, M92-220, Richland and Essex) to confirm the patterns observed.

Organism:

Glycine max

Type:

Genome variation profiling by genome tiling array

Platform:

GPL11198

10 Samples

Download data

(Submitter supplied) Soybean is a self-pollinating crop species that has relatively low nucleotide polymorphism rates compared to other crop plant species. Despite the appearance of a low intervarietal nucleotide polymorphism rate, a wide range of heritable phenotypic variation exists. There is even evidence for heritable phenotypic variation among individuals within some varieties. ‘Williams 82,’ the soybean variety used to produce the reference genome sequence, was derived from backcrossing a phytophthora root rot resistance locus from the donor parent ‘Kingwa’ into the recurrent parent ‘Williams.’ To explore the genetic basis of intravarietal variation, we investigated the nucleotide, structural and gene content variation of different Williams 82 individuals. more...

Organism:

Glycine max

Type:

Genome variation profiling by genome tiling array

Platform:

GPL11198

6 Samples

Download data: TIFF

(Submitter supplied) The Hydrophobic protein from soybean (HPS) locus is polymorphic among soybean cultivars and copy-number changes in the tandem array at this locus are directly correlated with expression level and seed coat luster phenotypes. Keywords: comparative genomic hybridization

Organism:

Glycine max

Type:

Genome variation profiling by array

Platform:

GPL3015

6 Samples

Download data: TIFF, TXT

(Submitter supplied) Background The homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental stresses. Many HD-Zip genes are characterized in Arabidopsis (Arabidopsis thaliana), and members of the family are being investigated for abiotic stress responses in rice (Oryza sativa), maize (Zea mays), poplar (Populus trichocarpa) and cucumber (Cucmis sativus). more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

21 Samples

Download data: TXT

(Submitter supplied) Ten mutants with altered seed composition traits were identified in a soybean fast neutron population (Bolon et al. 2014). These mutant lines were maintained to an advanced generation (ranging between M5 and M9) and compared to their wild-type parent (M92-220-Long) using CGH to identify the causative region/gene associated with the seed composition changes. 

Organism:

Glycine max

Type:

Genome variation profiling by array

Platform:

GPL22907

10 Samples

Download data: TXT

(Submitter supplied) According to the Canadian Food Inspection Agency and Health Canada, genetically modified crops are considered safe if they are substantially equivalent to a conventional crop in regards to agronomic, physiological and compositional characteristics. A recurring issue in safety assessment of genetically modified crops is the paucity of analytical methods to detect unintended or unexpected outcomes of genetic modification. more...

Organism:

Glycine max

Type:

Expression profiling by array

Dataset:

GDS3229

Platform:

GPL4592

25 Samples

Download data: CEL

Analysis of the first trifoliate leaves of two transgenic and three conventional soybean cultivars. To date, the possibility that transgene expression could lead to unintended effects remains a debated issue. Results provide insight into the overall molecular changes in transgenic soybean cultivars.

Organism:

Glycine max

Type:

Expression profiling by array, transformed count, 2 other, 5 strain sets

Platform:

GPL4592

Series:

GSE9374

25 Samples

Download data: CEL

(Submitter supplied) Agrobacterium tumefaciens-mediated genetic transformation has been routinely used in rice for more than a decade. However, the transformation efficiency of the indica rice variety is still unsatisfactory and much lower than that of japonica cultivars. Further improvement on the transformation efficiency lies in the genetic manipulation of the plant itself, which requires a better understanding of the underlying process accounting for the susceptibility of plant cells to Agrobacterium infection as well as the identification of plant genes involved in the transformation process. more...

Organism:

Oryza sativa Japonica Group; Oryza sativa; Oryza sativa Indica Group

Type:

Expression profiling by array

Platform:

GPL2025

36 Samples

Download data: CDF, CEL

(Submitter supplied) 1 RNA-Seq sample from Clark (PI548532) from seed coats of 100-200mg immature seeds

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

1 Sample

Download data: XLS

(Submitter supplied) 11 RNA-Seq samples from Williams (PI548631), with a variety of tissues especially immature seeds represented; 1 sample is from Williams 55, i mutation with black seed coat (PI547881)

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11192 GPL15008

12 Samples

Download data: XLSX