GEO DataSets

(Submitter supplied) Trimethylation of histone H3 lysine27 (H3K27me3) plays critical roles in regulating animal development, and in several cases, H3K27me3 is also required for the proper expression of developmentally important genes in plants. However, the extent to which H3K27me3 regulates plant genes on a genome-wide scale remains unknown. In addition, it is not clear whether the establishment and spreading of H3K27me3 occur through the same mechanisms in plants and animals. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL1979

4 Samples

Download data: CEL

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

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL1979

12 Samples

Download data: CEL

(Submitter supplied) Trimethylation of histone H3 lysine27 (H3K27me3) plays critical roles in regulating animal development, and in several cases, H3K27me3 is also required for the proper expression of developmentally important genes in plants. However, the extent to which H3K27me3 regulates plant genes on a genome-wide scale remains unknown. In addition, it is not clear whether the establishment and spreading of H3K27me3 occur through the same mechanisms in plants and animals. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL1979

4 Samples

Download data: CEL

(Submitter supplied) Trimethylation of histone H3 lysine27 (H3K27me3) plays critical roles in regulating animal development, and in several cases, H3K27me3 is also required for the proper expression of developmentally important genes in plants. However, the extent to which H3K27me3 regulates plant genes on a genome-wide scale remains unknown. In addition, it is not clear whether the establishment and spreading of H3K27me3 occur through the same mechanisms in plants and animals. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL1979

4 Samples

Download data: CEL

(Submitter supplied) 1. Oligo length: 36 2. Minimum oligonucleotide Tm: 80 3. Maximum oligonucleotide Tm: 95 4. Temperature to use during secondary structure prediction (an oligo will be rejected if it can fold into a stable secondary structure at this temperature): 65 5. Threshold to report putative cross-hybridizations (all targets hybridizing with a given oligo with a Tm exceeding this threshold are reported): 70 6. Minimum oligonucleotide GC content: 40 7. Maximum oligonucleotide GC content: 73 for gene models; 77 for TARs 8. Minimum distance between the 5' end of two adjacent oligos: 1 BAC fasta and description files linked as supplementary files

Organism:

Glycine max

2 Series

6 Samples

Download data: PDF, TXT

(Submitter supplied) 1. Oligo length: 36 2. Minimum oligonucleotide Tm: 80 3. Maximum oligonucleotide Tm: 95 4. Temperature to use during secondary structure prediction (an oligo will be rejected if it can fold into a stable secondary structure at this temperature): 65 5. Threshold to report putative cross-hybridizations (all targets hybridizing with a given oligo with a Tm exceeding this threshold are reported): 70 6. Minimum oligonucleotide GC content: 40 7. Maximum oligonucleotide GC content: 73 for gene models; 77 for TARs 8. Minimum distance between the 5' end of two adjacent oligos: 1 BAC fasta and description files linked as supplementary files

Organism:

Medicago truncatula

2 Series

6 Samples

Download data: PDF, TXT

(Submitter supplied) Background. Post-translational modifications of histones play important roles in regulating transcription by modulating the structural properties of the chromatin. In plants, methylation of histone H3 lysine4 (H3K4me) is associated with genes and required for normal plant development. Results. We have characterized the genome-wide distribution patterns of mono-, di- and trimethylation of H3K4 (H3K4me1, H3K4me2 and H3K4me3, respectively) in Arabidopsis thaliana using chromatin immunoprecipitation and high-resolution whole-genome tiling microarrays (ChIP-chip). more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7639

6 Samples

Download data: CEL

(Submitter supplied) Chromatin modification through the covalent modifications of histones play crucial role on establishment and propagation of gene expression pattern. Here we sought a global view of histone H3 modifications (tri-M-K4/27 and di-M-K27/36) and occupancy in Arabidopsis thaliana using ChIP combined with high-density tiling microarrays. In these analyses, we included vip3 mutant plants as well to gain an insight into role of Paf1C in plants. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL1979

24 Samples

Download data: CEL

(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) Dimethylation of histone H3 lysine 9 (H3K9m2) and trimethylation of histone H3 lysine 27 (H3K27m3) are two hallmarks of transcriptional repression in many organisms. In Arabidopsis thaliana, H3K27m3 is targeted by Polycomb Group (PcG) proteins and is associated with silent protein coding genes, while H3K9m2 is correlated with DNA methylation and is associated with transposons and repetitive sequences. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

2 Samples

Download data: WIG

(Submitter supplied) Dimethylation of histone H3 lysine 9 (H3K9m2) and trimethylation of histone H3 lysine 27 (H3K27m3) are two hallmarks of transcriptional repression in many organisms. In Arabidopsis thaliana, H3K27m3 is targeted by Polycomb Group (PcG) proteins and is associated with silent protein coding genes, while H3K9m2 is correlated with DNA methylation and is associated with transposons and repetitive sequences. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7143

6 Samples

Download data: PAIR

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

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by high throughput sequencing

Platforms:

GPL7143 GPL13222

8 Samples

Download data: PAIR, WIG

(Submitter supplied) Post-translational modifications of histones play important roles in modulating chromatin structure and regulating gene expression. We have previously shown that over two thirds of Arabidopsis genes contain histone H3 methylation at lysine-4 (H3K4me), and that tri-methylation of H3K4 (H3K4me3) is preferentially located at actively transcribed genes. In addition, several Arabidopsis mutants with locus-specific loss of H3K4me have been found to display various developmental abnormalities. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

6 Samples

Download data: CEL

(Submitter supplied) The POLYCOMB proteins are required for maintenance of silent chromatin states mediated by H3K27 trimethylation in animals, but POLYCOMB homologues are not found in plant genomes. Using DamID-chip, we found that the Arabidopsis chromodomain-containing protein LHP1 localizes to chromatin associated with H3K27me3 genome-wide. Furthermore, the LHP1 chromodomain binds H3K27me3 with high affinity. These results suggest that LHP1 shares similar functions with POLYCOMB. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL1979

8 Samples

Download data: CEL

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL6177 GPL3371

8 Samples

Download data: GFF, PAIR, TXT

(Submitter supplied) For the histone methylation analysis of undifferentiated and differentiated tissues a meristem enriched fraction and young leaves (up to 3 mm leaf blade length) were isolated from clavata3-9 plants. Clavata3-9 mutants harbour larger shoot apical meristems than wild type plants enabling the preparation of meristematic tissue by manual dissection. Samples from both tissues were used for expression and histone H3 lysine 27 trimethylation (H3K27me3) analysis. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL3371

4 Samples

Download data: GFF, PAIR, XLSX

(Submitter supplied) For the expression analysis of undifferentiated and differentiated tissues a meristem enriched fraction and young leaves (up to 3 mm leaf blade length) were isolated from clavata3-9 plants. Clavata3-9 mutants harbour larger shoot apical meristems than wild type plants enabling the preparation of meristematic tissue by manual dissection. Samples from both tissues were used for expression and histone H3 lysine 27 trimethylation (H3K27me3) analysis. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL6177

4 Samples

Download data: TXT, XLSX

(Submitter supplied) Methylation of lysine residues in the tail of the H3 histone is a key regulator of chromatin state and gene expression, conferred by a large family of enzymes containing an evolutionarily-conserved SET domain. One of the main types of SET domain proteins are those controlling H3K4 di- and trimethylation. The genome of Arabidopsis encodes 12 such proteins, including five ARABIDOPSIS TRITHORAX (ATX) proteins and seven ATX-Related (ATXR) proteins. more...

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL17639

12 Samples

Download data: BED, TXT, WIG

(Submitter supplied) rs05-12_setii - sdg25 and sdg26 - Differential transcriptome in mutant plants - seeds were sown in vitro and plantlets (Col0 wild type ,and n1, n2, n3, x123, sdg8, vip4,sdg25 and sdg26 mutants)were cultivated during 6 days (1.02 boyes stadge) Keywords: gene knock out

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL4346

12 Samples

Download data: GPR

(Submitter supplied) rs05-12_setii - all comparison - Differential transcriptome in mutant plants - seeds were sown in vitro and plantlets (Col0 wild type ,and n1, n2, n3, x123, sdg8, vip4,sdg25 and sdg26 mutants)were cultivated during 6 days (1.02 boyes stadge) Keywords: gene knock out

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL4346

22 Samples

Download data: GPR