Similar studies for GEO DataSets (Select 200104456) - GEO DataSets

Select item 2001044561.

Profiling of cytosine DNA-methylation in the Arabidopsis CAF-1 mutant fas2

(Submitter supplied) Chromatin Assembly Factor CAF-1 is a histone chaperone involved in nucleosome formation after replication. Here, cytosine DNA-methylation was profiled by bisulphite DNA sequencing in Arabidopsis wild type and the fas2 CAF-1 mutant. To test for transgenerational changes in DNA methylation, fas2 mutants of generation 1 and 6 were compared.

Organism:: Arabidopsis thaliana

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL13222
3 Samples

Download data: BW

Series

Accession:: GSE104456

ID:: 200104456

PubMed Similar studies SRA Run Selector

Select item 2000082792.

Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation

(Submitter supplied) Maintenance of CG methylation (mCG) patterns is essential for chromatin-mediated epigenetic regulation of transcription in plants and mammals. Using successive generations of an Arabidopsis thaliana mutant deficient in maintaining mCG, we found that mCG loss triggered genome-wide activation of alternative epigenetic mechanisms. However, these mechanisms involving RNA-directed DNA methylation, inhibiting expression of DNA demethylases, and retargeting of histone H3K9 methylation act in a stochastic and uncoordinated fashion. more...

Organism:: Arabidopsis thaliana

Type:: Methylation profiling by array

Platform:: GPL198
6 Samples

Download data: CEL, CHP, TXT

Series

Accession:: GSE8279

ID:: 200008279

Select item 2001042403.

Stable transgenerational epigenetic inheritance requires a DNA methylation-sensing circuit

(Submitter supplied) Eukaryotic genomes must maintain stable inheritance of epigenetic states. In plants, DNA methylation patterns are faithfully inherited over many generations but it is unknown how the dynamic activities of cytosine DNA methyltransferases and 5-methylcytosine DNA glycosylases, which remove 5-methylcytosine by base excision repair, interact to maintain epigenetic homeostasis. Here we show that a methylation-sensing gene regulatory circuit centered on a 5-methylcytosine DNA glycosylase gene is required for long-term epigenetic fidelity in Arabidopsis. more...

Organism:: Arabidopsis thaliana

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL13222
19 Samples

Download data: TXT

Series

Accession:: GSE104240

ID:: 200104240

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000871704.

DNA methylation inheritance across generations

(Submitter supplied) Cytosine DNA methylation regulates the expression of eukaryotic genes and transposable elements. Methylation is copied by DNA methyltransferases after DNA replication, which results in faithful transmission of methylation patterns during cell division and, at least in flowering plants, across generations. Trans-generational inheritance is mediated by a small group of cells that includes gametes and their progenitors. more...

Organism:: Arabidopsis thaliana

Type:: Methylation profiling by high throughput sequencing

Platforms:: GPL19580 GPL13222
10 Samples

Download data: GFF

Series

Accession:: GSE87170

ID:: 200087170

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000474905.

Selection of epigenetic variation in Arabidopsis [SNP data]

(Submitter supplied) In Arabidopsis thaliana a high rate of spontaneous epigenetic variation can occur in the DNA methylome in the absence of genetic variation and selection. It has been of great interest, whether natural epigenetic variation is subject to selection and contributes to fitness and adaptation in selective environments. We compared the variation in selected phenotypic traits, genome-wide cytosine DNA methylation and gene expression in two Arabidopsis recombinant inbred lines, which had undergone five generations of selection in experimental landscapes relative to their genetically identical ancestors. more...

Organism:: Arabidopsis thaliana

Type:: Genome variation profiling by high throughput sequencing

Platform:: GPL13222
9 Samples

Download data: TXT

Series

Accession:: GSE47490

ID:: 200047490

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000368456.

Selection of epigenetic variation in Arabidopsis [Bisulfite-Seq]

(Submitter supplied) In Arabidopsis thaliana a high rate of spontaneous epigenetic variation can occur in the DNA methylome in the absence of genetic variation and selection. It has been of great interest, whether natural epigenetic variation is subject to selection and contributes to fitness and adaptation in selective environments. We compared the variation in selected phenotypic traits, genome-wide cytosine DNA methylation and gene expression in two Arabidopsis recombinant inbred lines, which had undergone five generations of selection in experimental landscapes relative to their genetically identical ancestors. more...

Organism:: Arabidopsis thaliana

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL10088
8 Samples

Download data: TXT

Series

Accession:: GSE36845

ID:: 200036845

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000368447.

Selection of epigenetic variation in Arabidopsis [Expression]

(Submitter supplied) In Arabidopsis thaliana a high rate of spontaneous epigenetic variation can occur in the DNA methylome in the absence of genetic variation and selection. It has been of great interest, whether natural epigenetic variation is subject to selection and contributes to fitness and adaptation in selective environments. We compared the variation in selected phenotypic traits, genome-wide cytosine DNA methylation and gene expression in two Arabidopsis recombinant inbred lines, which had undergone five generations of selection in experimental landscapes relative to their genetically identical ancestors. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by array

Platform:: GPL14926
16 Samples

Download data: CEL, TXT

Series

Accession:: GSE36844

ID:: 200036844

PubMed Full text in PMC Similar studies

Select item 2000855518.

sRNA drives epigenetic changes in F1 hybrids

(Submitter supplied) Hybrid Arabidopsis plants undergo epigenetic reprogramming producing decreased levels of 24nt siRNAs and altered patterns of DNA methylation that can affect gene expression. Driving the changes in methylation are the processes Trans Chromosomal Methylation (TCM) and Trans Chromosomal deMethylation (TCdM). In TCM/TCdM the methylation state of one allele is altered to resemble the other allele. These changes in DNA methylation and the associated changes in small RNA levels in the F1 hybrid can be maintained in subsequent generations and affect hundreds of regions in the F2 epigenome. more...

Organism:: Arabidopsis thaliana

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

Platform:: GPL17639
38 Samples

Download data: CSV, TXT, WIG

Series

Accession:: GSE85551

ID:: 200085551

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001977189.

A balance of de novo and maintenance activities governs epigenetic inheritance of CG methylation in Arabidopsis transposons

(Submitter supplied) Dnmt1/MET1 methyltransferases mediate the epigenetic inheritance of cytosine methylation within CG dinucleotides (mCG). These enzymes use a semiconservative mechanism previously expected to produce binary present/absent methylation patterns. However, we show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG is quantitatively associated with transposon expression and is stably inherited across many generations. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL17639 GPL19580
80 Samples

Download data: TSV

Series

Accession:: GSE197718

ID:: 200197718

PubMed Similar studies

Select item 20003422210.

Methyl DIP-chip from self-pollinated ddm1 mutant and ddm1 kyp double mutant

(Submitter supplied) Methylation of histone H3 lysine 9 (H3K9me) and small RNA are associated with constitutively silent chromatin in diverse eukaryotes including plants. In plants, silent transposons are also marked by cytosine methylation, especially at non-CpG sites. The transposon-specific non-CpG methylation in plants is controlled by small RNA and H3K9me. Although it is often assumed that small RNA directs H3K9me,　interaction between small RNA and H3K9me has not been directly shown in plants. more...

Organism:: Arabidopsis thaliana

Type:: Methylation profiling by genome tiling array

Platforms:: GPL8080 GPL14974 GPL14975
18 Samples

Download data: PAIR

Series

Accession:: GSE34222

ID:: 200034222

Select item 20016634311.

Active DNA demethylation controls transgenerational epigenetic stability

(Submitter supplied) We examined spontaneously occurring variation in DNA methylation in wild type Col-0 plants, together with nrpd1 and ros1 mutants that are all propagated from single-seed descent for 10 generations.

Organism:: Arabidopsis thaliana

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL17639
35 Samples

Download data: BW

Series

Accession:: GSE166343

ID:: 200166343

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20008649812.

H3K23me1 is an evolutionary conserved histone modification associated with CG DNA methylation in Arabidopsis

(Submitter supplied) Amino-terminal tails of histones are targets for diverse post-translational modifications whose combinatorial action may constitute a code that will be read and interpreted by cellular proteins to define particular transcriptional states. Here, we describe monomethylation of histone H3 lysine 23 (H3K23me1) as a novel histone modification in plants. H3K23me1 is an evolutionary conserved mark in diverse flowering plant species. more...

Organism:: Arabidopsis thaliana

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL13222
12 Samples

Download data: BW

Series

Accession:: GSE86498

ID:: 200086498

PubMed Similar studies SRA Run Selector

Select item 20009407513.

The Arabidopsis DNA methylome is relatively impervious to abiotic stress

(Submitter supplied) Improving plant stress response holds great agricultural potential. One promising, yet speculative, possibility is the formation of plant stress memory facilitating enhanced responses to recurring stress. One possibility is the involvement of environmentally-induced variation in reversible chromatin marks, such as DNA methylation, leading to the altered regulation of underlying genetic elements that promote enhanced stress tolerance. more...

Organism:: Arabidopsis thaliana

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL17639
29 Samples

Download data: BED, COV

Series

Accession:: GSE94075

ID:: 200094075

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20000504314.

Arabidopsis CAF-1 depletion / gamma-irradiation

(Submitter supplied) CAF-1 is involved in nucleosome assembly following DNA replication and nucleotide excision repair. In Arabidopsis thaliana, the 3 CAF-1 subunits p150, p60 and p48 are encoded by FAS1, FAS2 and, most likely, MSI1, respectively.fas mutants exhibited increased levels of DNA double-strand breaks, a G2 phase retardation, and elevated levels of mRNAs coding for proteins involved in homologous recombinational repair. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by array

Platform:: GPL888
4 Samples

Download data

Series

Accession:: GSE5043

ID:: 200005043

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20002862715.

Profiling of small RNAs in Arabidopsis ovules

(Submitter supplied) We used profiling of Arabidopsis small RNA populations present in the mature ovules to define the potential genome targets of small RNAs during reproductive development. Defining the contributions and interactions of paternal and maternal genomes during embryo development is critical to understand the fundamental processes involved in hybrid vigor, hybrid sterility, and reproductive isolation. To determine the parental contributions and their regulation during Arabidopsis embryogenesis we combined deep-sequencing-based RNA profiling and genetic analyses. more...

Organism:: Arabidopsis thaliana

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL9062
1 Sample

Download data: TXT

Series

Accession:: GSE28627

ID:: 200028627

PubMed Similar studies SRA Run Selector

Select item 20002419816.

Deep-sequencing of total RNA from manually dissected wild-type and kyp-2m/KYPp Arabidopsis embryos

(Submitter supplied) This dataset provide deep-profiling of the embryonic transcriptome of total RNA at an early developmental stage (2-to-4 cells stage) and at the globular stage in Arabidopsis. Embryos were derived from either a cross between a Landsberg erecta (Ler) maternal parent and a Columbia (Col0) paternal parent or a cross between a kyp-2 Ler maternal parent and a Columbia paternal parent. Embryos were manually dissected ensuring no contamination with maternal seed coat or endosperm.

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL10088
6 Samples

Download data: TXT

Series

Accession:: GSE24198

ID:: 200024198

PubMed Similar studies SRA Run Selector

Select item 20015536917.

Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis

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

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Third-party reanalysis; Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL17639
19 Samples

Download data: TSV

Series

Accession:: GSE155369

ID:: 200155369

PubMed Full text in PMC Similar studies

Select item 20015536818.

Epigenetic reprogramming events rewire transcription during the alternation of generations in Arabidopsis [Small RNA-Seq]

(Submitter supplied) Alternation between morphologically distinct haploid and diploid life forms is a defining feature of most plant and algal life cycles, yet the underlying molecular mechanisms that govern these transitions remain unclear. Here, we explore the dynamic relationship between chromatin accessibility and epigenetic modifications during life form transitions in Arabidopsis. The diploid-to-haploid life form transition is governed by the loss of H3K9me2 and DNA demethylation of transposon-associated cis-regulatory elements. more...

Organism:: Arabidopsis thaliana

Type:: Non-coding RNA profiling by high throughput sequencing; Third-party reanalysis

Download data: BED, BW, XLSX

Series

Accession:: GSE155368

ID:: 200155368

PubMed Full text in PMC Similar studies

Select item 20015536719.

Epigenetic reprogramming events rewire transcription during the alternation of generations in Arabidopsis [DNA methylation]

(Submitter supplied) Alternation between morphologically distinct haploid and diploid life forms is a defining feature of most plant and algal life cycles, yet the underlying molecular mechanisms that govern these transitions remain unclear. Here, we explore the dynamic relationship between chromatin accessibility and epigenetic modifications during life form transitions in Arabidopsis. The diploid-to-haploid life form transition is governed by the loss of H3K9me2 and DNA demethylation of transposon-associated cis-regulatory elements, which is associated with dramatic changes in chromatin accessibility and transcriptional reprogramming. more...

Organism:: Arabidopsis thaliana

Type:: Methylation profiling by high throughput sequencing; Third-party reanalysis

Download data: BED, BW, XLSX

Series

Accession:: GSE155367

ID:: 200155367

PubMed Full text in PMC Similar studies

Select item 20015536520.

Epigenetic reprogramming events rewire transcription during the alternation of generations in Arabidopsis [RNA-Seq]

(Submitter supplied) Alternation between morphologically distinct haploid and diploid life forms is a defining feature of most plant and algal life cycles, yet the underlying molecular mechanisms that govern these transitions remain unclear. Here, we explore the dynamic relationship between chromatin accessibility and epigenetic modifications during life form transitions in Arabidopsis. The diploid-to-haploid life form transition is governed by the loss of H3K9me2 and DNA demethylation of transposon-associated cis-regulatory elements, which is associated with dramatic changes in chromatin accessibility and transcriptional reprogramming. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17639
12 Samples

Download data: TSV, TXT

Series

Accession:: GSE155365

ID:: 200155365

PubMed Full text in PMC Similar studies SRA Run Selector

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