GEO DataSets

(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) 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) 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) 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

Download data

(Submitter supplied) Background: Introduction of a transgene that transcribes RNA homologous to an endogenous gene in the plant genome can induce silencing of both genes, a phenomenon termed cosuppression. Cosuppression was first discovered in transgenic petunia plants transformed with the CHS-A gene encoding chalcone synthase, in which nonpigmented sectors in flowers or completely white flowers are produced. Some of the flower-color patterns observed in transgenic petunias having CHS-A cosuppression resemble those in existing nontransgenic varieties. more...

Organism:

Petunia x hybrida

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16386

4 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:

GPL11192 GPL15008

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) 22-nucleotide (nt) microRNAs (miRNAs) derived from asymmetric duplexes trigger trans-acting phased small interfering RNA (tphasiRNA) production from complementary targets. Here we investigate the efficacy of 22-nt artificial miRNA (amiRNA) mediated RNA silencing relative to conventional hairpin RNA (hpRNA) and 21-nt amiRNA mediated RNA silencing. CHALCONE SYNTHASE (CHS) was selected as a target in Arabidopsis thaliana due to the obvious and non-lethal loss of anthocyanin accumulation upon widespread RNA silencing. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9302

4 Samples

Download data: CSV, TXT

(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

Download data

(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) Copy number expansions such as amplifications and duplications contribute to human phenotypic variation, promote molecular diversification during evolution, and drive the initiation and/or progression of various cancers. The mechanisms underlying these copy number changes are still incompletely understood, however. We recently demonstrated that transient, limited re-replication from a single origin in Saccharomyces cerevisiae efficiently induces segmental amplification of the re-replicated region. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by genome tiling array

Platform:

GPL3412

333 Samples

Download data: GPR

(Submitter supplied) In a study to elucidate the genetic defects in patients with X-linked intellectual disability (XLID) we performed X chromosome-specific BAC-array-CGH and identified 0.33 to 1.0 Mb nonrecurrent copy number gains at Xp11.22 in affected males of unrelated XLID families. All aberrations segregate with the disease in the families and the carrier mothers show a nonrandom X-inactivation. Affected males suffered from mild to moderate ID. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL14729

8 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) Array CGH analysis in order to determine the size of atypical NF1 deletions under investigation

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL18714

12 Samples

Download data: TXT

(Submitter supplied) Array-CGH analysis of X chromosome of XLMR patient Keywords: comparative genomic hybridization

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL5857 GPL5866

3 Samples

Download data: GPR