GEO DataSets

(Submitter supplied) The soybean (Glycine max) seed coat has distinctive, genetically programmed patterns of pigmentation and the recessive k1 mutation can epistatically overcome the dominant I and i-i alleles, which inhibit seed color by producing small interfering RNAs (siRNAs) targeting chalcone synthase (CHS) mRNAs. Small RNA sequencing of dissected regions of immature seed coats demonstrated that CHS siRNA levels cause the patterns produced by the i-i and i-k alleles of the I locus, which restrict pigment to the hilum or saddle region of the seed coat, respectively. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

12 Samples

Download data: TXT

(Submitter supplied) The soybean (Glycine max) seed coat has distinctive, genetically programmed patterns of pigmentation and the recessive k1 mutation can epistatically overcome the dominant I and i-i alleles, which inhibit seed color by producing small interfering RNAs (siRNAs) targeting chalcone synthase (CHS) mRNAs. Small RNA sequencing of dissected regions of immature seed coats demonstrated that CHS siRNA levels cause the patterns produced by the i-i and i-k alleles of the I locus, which restrict pigment to the hilum or saddle region of the seed coat, respectively. more...

Organism:

Glycine max

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15008

16 Samples

Download data: TXT

(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:

GPL15008 GPL11192

17 Samples

Download data: TXT

(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) We present results from deep sequencing of small RNA populations from several genotypes of soybean and demonstrate that the CHS siRNAs accumulated only in the seed coats of the yellow varieties having either the dominant I or i-i alleles and not in the pigmented seed coats with homozygous recessive i genotypes. However, the diagnostic CHS siRNAs did not accumulate in the cotyledons of genotypes with the dominant I or i-i alleles thus demonstrating the novelty of an endogenous inverted repeat region of CHS genes driving RNA silencing in trans of non-linked CHS family members in a tissue-specific manner. more...

Organism:

Glycine max

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10267

4 Samples

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(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) 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

(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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL15008

16 Samples

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(Submitter supplied) We determined the molecular basis of three soybean lines that vary in seed coat color at the R locus which is thought to encode a MYB transcription factor. RM55-rm is homozygous for a mutable allele (rm) that specifies black and brown striped seeds; RM30-R* is a stable black revertant isoline derived from the mutable line; and RM38-r has brown seed coats due to a recessive r allele shown to translate a truncated MYB protein. more...

Organism:

Glycine max

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15008

2 Samples

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(Submitter supplied) We determined the molecular basis of three soybean lines that vary in seed coat color at the R locus which is thought to encode a MYB transcription factor. RM55-rm is homozygous for a mutable allele (rm) that specifies black and brown striped seeds; RM30-R* is a stable black revertant isoline derived from the mutable line; and RM38-r has brown seed coats due to a recessive r allele shown to translate a truncated MYB protein. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

14 Samples

Download data: TXT

(Submitter supplied) The plant cell wall performs a number of essential functions including providing shape to many different cell types and serving as a defense against potential pathogens. The net pattern mutation creates breaks in the seed coat of soybean (Glycine max) because of ruptured cell walls. Using RNA-Seq, we examined the seed coat transcriptome from three stages of immature seed development in two pairs of isolines with normal or defective seed coat phenotypes due to the net pattern. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11192 GPL15008

12 Samples

Download data: TXT

(Submitter supplied) Seed coat colour is determined by the type of pigment deposited in the seed coat cells. It is related to important agronomic traits of seeds, such as seed dormancy, longevity, oil content, protein content and fibre content. In Brassica napus, inheritance of seed coat colour is related to maternal effects and pollen effects (xenia effects). In this research, we isolated a mutation of yellow seeded B. more...

Organism:

Brassica napus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15579

2 Samples

Download data: FASTA, XLS

(Submitter supplied) Background: To elucidate features of seed development, we investigated the transcriptome of a soybean isoline from the germplasm collection that contained an introgressed allele known as minute hilum (mi) which confers a smaller hilum region where the seed attaches to the pod and also results in seed coat cracking surrounding the hilum region. Results: RNAs were extracted from immature seed from an extended hilum region (i.e., the hilum and a small ring of tissue surrounding the hilum in which the cracks form) at three different developmental stages:10-25, 25-50 and 50-100 mg seed fresh weight in two independent replicates for each stage. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

20 Samples

Download data: XLSX

(Submitter supplied) Maize LEAFBLADELESS1 (LBL1) and Arabidopsis SUPPRESSOR OF GENE SILENCING3 (SGS3) play orthologous roles in the biogenesis of 21 nucleotide trans-acting short-interfering RNAs (tasiRNAs). The phenotypes conditioned by mutation of lbl1 and SGS3 are, however, strikingly different, suggesting that the activities of these small RNA biogenesis components, or the tasiRNAs and their targets might not be entirely conserved. more...

Organism:

Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL13977 GPL15463

10 Samples

Download data: TXT, XLS

(Submitter supplied) 9,216 single-spotted cDNA clones from embryo, seed coat, flower and whole pod libraries Keywords = soybean

Organism:

Glycine max

5 Series

131 Samples

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