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Arabidopsis thaliana

ABSTRACT: Methylation Changes in Arabidopsis seed development

PROVIDER: PRJNA281872 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1984602.fastq.gz	Fastqsanger.gz
	SRR1984603.fastq.gz	Fastqsanger.gz
	SRR1984604.fastq.gz	Fastqsanger.gz
	SRR1984605.fastq.gz	Fastqsanger.gz
	SRR1984606.fastq.gz	Fastqsanger.gz

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Arabidopsis thaliana

Project description:Methylation Changes in Arabidopsis Mature Green Seed Parts

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Methylation Changes in Arabidopsis seed development

Project description: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. Illumina sequencing of bisulfite-converted genomic DNA from six seed developmental stages in Arabidopsis: global stage (glob), linear cotyledon stage (lcot), mature green stage (mg), post mature green stage (pmg), dry seed (dry) and leaves (leaf) from 4 week plant.

2015-04-22 | E-GEOD-68132 | biostudies-arrayexpress

Methylation Changes in Arabidopsis Mature Green Seed Parts

Project description: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. Each seed part undergoes distinct developmental programs during seed development. What methylation changes occur in the different seed parts, if any, remains unknown. To uncover the possible role of DNA methylation in different parts of the seed, we characterized the methylome of two major parts of Arabidopsis mature green stage seeds, the seed coat and embryo, using Illumina sequencing. Illumina sequencing of bisulfite-converted genomic DNA from two parts of Arabidopsis mature green seeds: seed coat (SC) and embryo (EMB).

2014-05-17 | E-GEOD-57755 | biostudies-arrayexpress

Methylation Changes in Arabidopsis seed development

2015-04-22 | GSE68132 | GEO

Arabidopsis thaliana

Project description:Gene expression during seed coat development in Arabidopsis

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Karrikin responses in Arabidopsis thaliana seed

Project description:Karrikins promote seed germination in Arabidopsis thaliana. Completion of germination (protrusion of the radicle) is not observed until ~72 h in dormant wildtype seed under these conditions. We used microarrays to examine karrikin-induced transcriptional changes after 24 h of imbibition. Transcriptional changes may indicate events leading to karrikin-induced germination or karrikin-specific markers.

2010-03-01 | GSE20556 | GEO

Arabidopsis thaliana

Project description:Seed development

| PRJNA120379 | ENA

Methylation Profile of dry seed from Arabidopsis ddcc mutant

Project description: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 methylome of ddcc mutant in Arabidopsis dry seed using Illumina sequencing. Meanwhile, vegetative tissue, leaves from 3 week plant with ddcc mutant and from wild type, and dry seed from wild type plant were used as control. Illumina sequencing of bisulfite-converted genomic DNA from dry seed and 3-week-plant leaves of ddcc mutant and wild type.

2015-04-22 | E-GEOD-68131 | biostudies-arrayexpress

sRNA-seq data over Arabidopsis thaliana germination

Project description:sRNA-seq profiling of 10 time points during germination in Arabidopsis, from freshly harvested seed, through mature seed, stratification, germination and to post-germination.

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Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting: small RNA-seq profiling in Arabidopsis thaliana Col, Ler, and Cvi parental and reciprocal F1 hybrid seeds

Project description:Imprinted gene expression occurs during seed development in plants and is associated with differential DNA methylation of parental alleles, particularly at proximal transposable elements (TEs). Imprinting variability could contribute to observed parent-of-origin effects on seed development. We investigated intraspecific variation in imprinting, coupled with analysis of DNA methylation and small RNAs, among three Arabidopsis strains with diverse seed phenotypes. The majority of imprinted genes were parentally biased in the same manner among all strains. However, we identified several examples of allele-specific imprinting correlated with intraspecific epigenetic variation at a TE. We successfully predicted imprinting in additional strains based on methylation variability. We conclude that there is standing variation in imprinting even in recently diverged genotypes due to intraspecific epiallelic variation. These data demonstrate that epiallelic variation and genomic imprinting intersect to produce novel gene expression patterns in seeds.

2014-07-08 | GSE52807 | GEO

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