GEO DataSets

(Submitter supplied) We report the genome-wide transcriptome of soybean seeds across several stages of seed development and the entire life cycle using Illumina high-throughput sequencing technology. Specifically, we profiled whole seeds containing globular-stage, heart-stage, cotyledon-stage, early maturation-stage, mid-maturation-stage, and late-maturation-stage embryos. We also profiled dry soybean seeds, and vegetative and reproductive tissues including leaves, roots, stems, seedlings, and floral buds.

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

12 Samples

Download data: TXT

(Submitter supplied) The role of on-CG methylation in seed development and dormancy remains unknown. There are four genes in charge of non-CG methylation in Arabidopsis: drm1, drm2, cmt2 and cmt3. The majority of non-CG methylation in vegetative tissues, leaf, is gone in homozygous ddcc mutant line (Hume et al., 2014). To uncover the possible role of non-CG DNA methylation in seed development and dormancy, we characterized the transcriptome of ddcc mutant in Arabidopsis post-mature green seeds using Illumina sequencing. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

4 Samples

Download data: TXT

(Submitter supplied) There are four major seed developmental phases in Arabidopsis seed development: morphogenesis, maturation, dormancy and germination. What methylation changes occurring in the different phases, if any, remains unknown. To uncover the possible role of DNA methylation in different parts of the seed, we characterized the methylome of four major seed developmental phases of Arabidopsis using Illumina sequencing: global stage (glob) and linear cotyledon stage (lcot) for morphogenesis phase; mature green stage (mg) and post mature green stage (pmg) for maturation phase; dry seed (dry) for dormancy phase; leaves (leaf) from 4 week plant for vegetative tissues.

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13222

6 Samples

Download data: TXT

(Submitter supplied) The role of non-CG methylation in seed development and dormancy remains unknown. There are four genes in charge of non-CG methylation in Arabidopsis: drm1, drm2, cmt2 and cmt3. The majority of non-CG methylation in vegetative tissues, leaf, is gone in homozygous ddcc mutant line (Hume et al., 2014). To uncover the possible role of non-CG DNA methylation in seed development and dormancy, we characterized the methylome of ddcc mutant in Arabidopsis postmature-green-stage seed and dry seed using Illumina sequencing. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13222

6 Samples

Download data: TXT

(Submitter supplied) Seeds are comprised of three major parts of distinct parental origin: the seed coat, embryo, and endosperm. The maternally-derived seed coat is important for nurturing and protecting the seeds during development. By contrast, the embryo and the endosperm are derived from a double fertilization event, where one sperm fertilizes the egg to form the diploid zygote and the other sperm fertilizes the central cell to form the triploid endosperm. more...

Organism:

Glycine max

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15008

3 Samples

Download data: TXT

(Submitter supplied) Seeds are comprised of three major parts of distinct parental origin: the seed coat, embryo, and endosperm. The maternally-derived seed coat is important for nurturing and protecting the seeds during development. By contrast, the embryo and the endosperm are derived from a double fertilization event, where one sperm fertilizes the egg to form the diploid zygote and the other sperm fertilizes the central cell to form the triploid endosperm. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13222

2 Samples

Download data: TXT

(Submitter supplied) We investigated soybean seed development because (1) soybean seeds are a major source of food and fuel, (2) soybean seeds have been an excellent system for studying the basic processes controlling seed development for over three decades, and (3) new soybean genomic resources, including the sequence of the soybean genome and the gene expression profiles for all seed compartments, tissues, and cell types, can be used to gain new insights into the regulatory processes required for seed differentiation. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

51 Samples

Download data: TXT

(Submitter supplied) Seeds are comprised of three majors parts of distinct parental origin: the seed coat, embryo, and endosperm. The maternally-derived seed coat is important for nurturing and protecting the seeds during development. By contrast, the embryo and the endosperm are derived from a double fertilization event, where one sperm fertilizes the egg to form the diploid zygote and the other sperm fertilizes the central cell to form the triploid endosperm. more...

Organism:

Glycine max

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15008

3 Samples

Download data: TXT

(Submitter supplied) Seeds are comprised of three majors parts of distinct parental origin: the seed coat, embryo, and endosperm. The maternally-derived seed coat is important for nurturing and protecting the seeds during development. By contrast, the embryo and the endosperm are derived from a double fertilization event, where one sperm fertilizes the egg to form the diploid zygote and the other sperm fertilizes the central cell to form the triploid endosperm. more...

Organism:

Glycine max

Type:

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

Platform:

GPL15008

10 Samples

Download data: TXT

(Submitter supplied) What methylation changes are occurring in different compartments of early maturation stage seed largely remains unknown. To uncover the possible role of DNA methylation in different compartments of early maturation stage seed, we characterized the methylome of two major compartments (abaxial parenchyma and adaxial parenchyma) in embryonic cotyledon, four major compartments (parenchyma, plumule, root tip, and vascular) in embryonic axis, and seed coat layers (parenchyma and palisade) using Illumina sequencing. more...

Organism:

Glycine max

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15008

10 Samples

Download data: TXT

(Submitter supplied) What methylation changes are occurring during seed development largely remains unknown. To uncover the possible role of DNA methylation throughout all of seed development - from fertilization through dormancy and post-germination in soybean, we characterized the methylome of whole seeds representing the differentiation (GLOB and COT stages), maturation (early- [EM], mid- [B1] and late- [AA1] maturation stages), dormancy (DRY stage), and post-germination (seedling) phases of soybean seed development using Illumina sequencing. more...

Organism:

Glycine max

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15008

18 Samples

Download data: TXT

(Submitter supplied) How epigenetics is involved in the transition from seed maturation to seed germination largely remains elusive. To uncover the possible role of epigenetics in gene expression during the transition from seed maturation to seed germination in soybean, the transcriptome of cotyledons from four stages of soybean seed maturation and germination, including mid-late maturation, late maturation, seed dormancy and seed germination, were profiled by Illumina sequencing. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11192

4 Samples

Download data: TXT

(Submitter supplied) In order to describe the molecular phenotype of spch-5 and to explore possible changes in gene expression underlying the effects on its epidermal development of BL treatment, we performed a microarray-based transcriptomic analysis. Using 3-days old seedlings grown in the absence or presence of BL, we compared the transcriptomic profiles of wild type (Col-0) and spch-5 plants. In addition, we analyzed a SPCHPPP-complemented spch-3 line to identify gene expression changes distinct of spch-5 or common to the two SPCH variants. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL22511

16 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13222

13 Samples

Download data: WIG

(Submitter supplied) Lineage-specific stem cells are critical for the production and maintenance of specific cell types and tissues in multicellular organisms. In higher plants, the initiation and proliferation of stomatal stem cells is controlled by the basic helix-loop-helix transcription factor SPEECHLESS (SPCH). The stomatal stem cells and SPCH, which represent an innovation in seed plants, allow flexibility in the production of stomata, but how SPCH generates these stem cells is unclear. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

11 Samples

Download data: TXT

(Submitter supplied) Lineage-specific stem cells are critical for the production and maintenance of specific cell types and tissues in multicellular organisms. In higher plants, the initiation and proliferation of stomatal stem cells is controlled by the basic helix-loop-helix transcription factor SPEECHLESS (SPCH). The stomatal stem cells and SPCH, which represent an innovation in seed plants, allow flexibility in the production of stomata, but how SPCH generates these stem cells is unclear. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13222

2 Samples

Download data: WIG

(Submitter supplied) Environmental factors shape the phenotypes of multicellular organisms. The production of stomata—the epidermal pores required for gas exchange in plants—is highly plastic, and provides a powerful platform to address environmental influence on cell differentiation [1-3]. Rising temperatures are already impacting plant growth, a trend expected to worsen in the near future [4]. High temperature inhibits stomatal production but the underlying mechanism is not known [5]. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

16 Samples

Download data: TXT

(Submitter supplied) The life cycle of flowering plants ends and begins with seeds. Unlike animals, plants can pause their life cycle as dormant seeds during this transition. DNA methylation is involved in the regulation of gene expression and genome integrity. Reprogramming erases and re-establishes DNA methylation during development in animals. Knowledge of reprogramming or reconfiguration in plants has been limited to pollen and the central cell. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17639

24 Samples

Download data: TSV

(Submitter supplied) In plants, transposons and non-protein-coding repeats are epigenetically silenced by CG and non-CG methylation. This pattern of methylation is mediated in part by small RNAs and two specialized RNA polymerases, Pol IV and Pol V, in a process called RNA-directed DNA methylation. By contrast, many protein-coding genes transcribed by Pol II contain in their gene bodies exclusively CG methylation that is independent of small RNAs and Pol IV/Pol V activities. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9302

3 Samples

Download data: TXT

(Submitter supplied) Precise cell division control is critical for developmental patterning. For the differentiation of a functional stoma, a cellular valve for efficient gas exchange, the single symmetric division of an immediate precursor is absolutely essential. Yet, the mechanism governing the single division event remains unclear. Here we report the complete inventories of gene expression by the Arabidopsis bHLH protein MUTE, a potent inducer of stomatal differentiation. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

6 Samples

Download data: TXT