GEO DataSets

(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) 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) Evaluation of transcripts from soybean seed tissue during seed fill for a pair of near-isogenic lines contrasting in seed protein and oil and carrying an introgression at the linkage group I protein QTL region. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Yung-Tsi Bolon. The equivalent experiment is GM11 at PLEXdb.]

Organism:

Glycine max

Type:

Expression profiling by array

Platform:

GPL4592

24 Samples

Download data: CEL

(Submitter supplied) see Vodkin et al., BMC Genomics 5:73 (2004) for details of cDNAs represented on the arrays and Thibaud-Nissen et al., Plant Physiol 132:118-136 (2003); Zou et al. Mol Plant Microbe Interat 18:1161-1174 (2005); Zabala and Vodkin, Plant Cell 17: 2619-2632 (2005) for use of cDNA arrays in soybean. Protocol: PCR amplified cDNA inserts printed with Genemachines Omnigrid

Organism:

Glycine max

6 Series

82 Samples

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(Submitter supplied) see Vodkin et al., BMC Genomics 5:73 (2004) for details of cDNAs represented and Thibaud-Nissan, et al., Plant Physiol 132: 118-136 (2003); and Zabala and Vodkin, Plant Cell 17: 2619-2632 (2005) for use of cDNA arrays in soybean Protocol: amplified cDNAs printed with Genemachines Omnigrid

Organism:

Glycine max

12 Series

191 Samples

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(Submitter supplied) In a previous study, seed coat and cotyledon tissues of Williams, Richland and T157 soybean lines were investigated to show tissue specificity of CHS siRNA expression (Tuteja et al., 2009). Here, we investigated more tissues such as leaf, root and germinating cotyledon to ascertain the tissue specificity of CHS siRNAs in Williams. Data from multiple small RNA libraries were sequenced deeply by the Illumina high-throughput sequencing technology. more...

Organism:

Glycine max

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL15008 GPL11192

8 Samples

Download data: TXT

(Submitter supplied) The I locus is a 27-kb inverted repeat cluster of chalcone synthase genes CHS1-3-4 that mediates siRNA down-regulation of CHS7 and CHS8 target mRNAs during seed development leading to yellow seed coats lacking anthocyanin pigments. Here, we report small RNA sequencing of ten stages of seed development from a few days post fertilization through maturity, revealing the amplification from primary to secondary short interfering RNAs (siRNAs) occurring during development. more...

Organism:

Glycine max

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL11192 GPL15008

17 Samples

Download data: TXT

(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) Five degradome libraries were constructed from three different seed developmental stages. Separate degradome libraries were constructed for seed coat and cotyledons to identify the tissue specific miRNAs and their potential targets. Sequencing and analysis of degradome libraries gives identification of 183 different targets for 80 known soybean miRNAs. We found 30 cotyledon specific, 18 seed coat specific and 32 miRNAs found in both tissues irrespective of the developmental stages. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

5 Samples

Download data: TXT

(Submitter supplied) Transformation of Glycine max with seed-targeted expression vectors via Agrobacterium causes measurable unscripted gene expression changes in the seed transcriptome

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

36 Samples

Download data: GTF

(Submitter supplied) 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).

Organism:

Glycine max

Type:

Expression profiling by array

Platform:

GPL4592

6 Samples

Download data: CEL, TXT

(Submitter supplied) Seed germination is important to soybean (Glycine max) growth and development, ultimately affecting soybean yield. A lower seed field emergence has been the main hindrance for breeding soybeans low in phytate. Although this reduction could be overcome by additional breeding and selection, the mechanisms of seed germination in different low phytate mutants remain unknown. In this study, we performed a comparative transcript analysis of two low phytate soybean mutants (TW-1 and TW-1-M), which have the same mutation, a 2 bp deletion in GmMIPS1, but show a significant difference in seed field emergence.

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21998

18 Samples

Download data: TXT

(Submitter supplied) An overview of small RNAs sequences existing in seed development and contrasted with vegetative tissues of the soybean

Organism:

Glycine max

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10267

4 Samples

Download data: TXT

(Submitter supplied) Gene expression profiles in soybean seeds at 4 developmental stages, pod, bean 2 mm, bean 5 mm, and full-sized bean, were examined by DNA microarray analysis. Total genes of each samples were classified into 4 clusters according to developmental stages. Differentially expressed genes (DEGs) were extracted by comparing their expression in two adjacent stages, by using the rank product method. To characterize the gene expression during seed development, DEGs were sorted into 8 clusters by the hclust function, according to gene expression patterns. more...

Organism:

Glycine max

Type:

Expression profiling by array

Platform:

GPL4592

8 Samples

Download data: CEL, CHP