GEO DataSets

(Submitter supplied) CHD3 proteins are ATP-dependent chromatin remodeling factors that are components of diverse multisubunit complexes that can either repress or activate gene expression. In plants, the CHD3 protein PICKLE (PKL) is necessary for repression of seed-specific genes during germination and promotes deposition of the repressive epigenetic mark trimethylation of histone H3 lysine 27 (H3K27me3). It is unknown, however, if PKL acts directly at H3K27me3-enriched loci. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

6 Samples

Download data: CEL

(Submitter supplied) Relative expression data from germinating seeds of Columbia (wt), the pkl mutant (pkl), Columbia plus uniconazole-P (Uwt) and the pkl-mutant plus uniconazole-P (Upkl).

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Dataset:

GDS3425

Platform:

GPL198

24 Samples

Download data: CEL, TXT

Analysis of pickle (pkl) mutant seedlings treated with the gibberellin (GA) inhibitor uniconazole. PKL encodes a CHD3 chromatin remodeler that acts during germination to repress the expression of seed-associated genes. Repression of seed-associated traits is promoted in pkl mutant seedlings by GA.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array, count, 2 agent, 2 genotype/variation sets

Platform:

GPL198

Series:

GSE11852

24 Samples

Download data: CEL

(Submitter supplied) Relative expression data from germinating seeds of Columbia (wt), the pkl mutant (pkl), Columbia plus uniconazole-P (Uwt) and the pkl-mutant plus uniconazole-P (Upkl). Each experimental condition (wt, pkl, Uwt and Upkl) has four true replicates for a total of 16 chips. Keywords = CHD3 Keywords = chromatin remodeling factors Keywords = developmental transition Keywords = embryo Keywords = seed germination Keywords: other

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Dataset:

GDS378

Platform:

GPL71

16 Samples

Download data

Analysis of effect of uniconazole-P, a gibberellin biosynthetic inhibitor, on wild type and pickle (pkl) germinating seeds. pkl mutants are defective in repressing embryonic differentiation characteristics. Gibberellins promote germination of seeds.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array, count, 2 agent, 2 strain sets

Platform:

GPL71

Series:

GSE277

16 Samples

Download data

(Submitter supplied) ChIP-seq was performed using anti-H3, anti-H3K27me3, and anti-H2A.Z antibodies in three-week-old WT, pkl-1, clf-28, and pie1-5 shoots using paired-end sequencing. Strand-specific RNA-seq was performed on RNA extracted from the same biological samples.

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL17639

44 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Nucleation and spreading of H3K27me3 are critical steps for the initiation and maintenance, respectively, of mitotically inheritable Polycomb-mediated repressive chromatin states in cell identity memory, in both animals and plants. Although a semiconservative read-and-write mechanism is proposed to play a key role in H3K27me3 propagation, the specific determinant and underlying mechanism by which the Polycomb Repressive Complex 2 (PRC2) accesses unmodified nucleosomes for propagating H3K27me3 remain enigmatic. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

12 Samples

Download data: TXT

(Submitter supplied) Nucleation and spreading of H3K27me3 are critical steps for the initiation and maintenance, respectively, of mitotically inheritable Polycomb-mediated repressive chromatin states in cell identity memory, in both animals and plants. Although a semiconservative read-and-write mechanism is proposed to play a key role in H3K27me3 propagation, the specific determinant and underlying mechanism by which the Polycomb Repressive Complex 2 (PRC2) accesses unmodified nucleosomes for propagating H3K27me3 remain enigmatic. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26208

4 Samples

Download data: BIGWIG

(Submitter supplied) The Polycomb repressive complex 2 (PRC2) is an essential epigenetic regulator that deposits repressive H3K27me3 for transcriptional gene silencing in eukaryotes. The PRC2-mediated gene silencing process occurs in two steps: the initial H3K27me3 deposition at the nucleation region, and the subsequent spreading of H3K27me3 over the entire gene. Lack of H3K27me3 spreading gives rise to a metastable state that could lead to loss of silencing. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26208

19 Samples

Download data: BIGWIG

(Submitter supplied) The Polycomb repressive complex 2 (PRC2) is an essential epigenetic regulator that deposits repressive H3K27me3 for transcriptional gene silencing in eukaryotes. The PRC2-mediated gene silencing process occurs in two steps: the initial H3K27me3 deposition at the nucleation region, and the subsequent spreading of H3K27me3 over the entire gene. Lack of H3K27me3 spreading gives rise to a metastable state that could lead to loss of silencing. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26208

89 Samples

Download data: BIGWIG

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

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL26208

124 Samples

Download data: BIGWIG

(Submitter supplied) SPLAYED (SYD) is a SWItch/Sucrose Non-Fermentable (SWI/SNF)-type chromatin remodeler identified in Arabidopsis thaliana (Arabidopsis). It is believed to play both redundant and differential roles with its closest homolog BRAHMA (BRM) in diverse plant growth and development processes. To better understand how SYD functions, we profiled the genome-wide occupancy of SYD and its impact on the global transcriptome and deposition of trimethylation of histone H3 on lysine 27 (H3K27me3). more...

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL21785 GPL17639

15 Samples

Download data: BW, TXT

(Submitter supplied) Transcriptional profiling of 6-day-old seedlings of Arabidopsis wild type control and zrf1 mutants is performed using Agilent's Whole Arabidopsis Gene Expression Microarray (4x44K).

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL12621

8 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10918 GPL10911

32 Samples

Download data: PAIR

(Submitter supplied) a2e_fie - h3k4me3_wt_col_seedlings_db - Epigenomic mapping in fie - Genome-wide epigenomic mapping Keywords: chip-chip

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10918 GPL10911

8 Samples

Download data: PAIR

(Submitter supplied) a2e_fie - h3k4me3_fie_col_seedlings_db - Epigenomic mapping in fie - Genome-wide epigenomic mapping Keywords: chip-chip

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10911 GPL10918

8 Samples

Download data: PAIR

(Submitter supplied) a2e_fie - h3k27me3_wt_col_seedlings_db - Epigenomic mapping in fie - Genome-wide epigenomic mapping Keywords: chip-chip

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10918 GPL10911

8 Samples

Download data: PAIR

(Submitter supplied) a2e_fie - h3k27me3_fie_col_seedlings_db - Epigenomic mapping in fie - Genome-wide epigenomic mapping Keywords: chip-chip

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10911 GPL10918

8 Samples

Download data: PAIR

(Submitter supplied) rs09-08_fie - upregulation of transcripts in the absence of prc2 repressory complex - Role of PRC2 repressory complex for differentiation pathways in Arabidopsis thaliana? - Comparison of transcriptome between two biological replicates of fie mutants in comparison with two biological replicates of Col WT. Keywords: gene knock out

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL9553

12 Samples

Download data: GPR

(Submitter supplied) H3K27me3 is a repressive chromatin mark of genes and is catalyzed by homologs of Enhancer of zeste [E(z)], a component of Polycomb-repressive complex 2 (PRC2), while DNA methylation that occurs in CG and non-CG (CHG and CHH, where H is A, C or T) contexts is a hallmark of transposon silencing in plants. However, relationship between H3K27me3 and DNA methylation in gene repression remains unclear. In addition, the mechanism of PRC2 recruitment to specific genes is not known in plants. more...

Organism:

Oryza sativa Japonica Group

Type:

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

Platforms:

GPL13834 GPL22250

7 Samples

Download data: TAR, TXT, WIG