GEO DataSets

(Submitter supplied) Plants respond to environmental challenges via a network of signalling pathways. Early responses prevent damage if the stress persists but delay growth in fluctuating conditions. Optimizing these trade-offs requires tunability of plant responsiveness to environmental signals. We have previously shown that Histone Deacetylation Complex 1 (HDC1), which interacts with multiple proteins in histone deacetylation complexes, regulates the sensitivity of Arabidopsis seedlings to salt and ABA, but the underlying mechanism remained elusive. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19580

18 Samples

Download data: CSV

(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:

GPL19580

22 Samples

Download data: BEDGRAPH, CSV

(Submitter supplied) Plants respond to environmental challenges via a network of signalling pathways. Early responses prevent damage if the stress persists but delay growth in fluctuating conditions. Optimizing these trade-offs requires tunability of plant responsiveness to environmental signals. We have previously shown that Histone Deacetylation Complex 1 (HDC1), which interacts with multiple proteins in histone deacetylation complexes, regulates the sensitivity of Arabidopsis seedlings to salt and ABA, but the underlying mechanism remained elusive. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19580

4 Samples

Download data: BEDGRAPH

(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

Platforms:

GPL23157 GPL17639

16 Samples

Download data: BW

(Submitter supplied) To investigate how HDC1, HDA6, and HDA19 regulate gene transcription and flowering time in short day conditions, we performed RNA deep sequencing (RNA-seq) to compare the transcriptomes of wild type, hdc1, hda6, and hda19 mutants grown in short day conditions with two biological repeats.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23157

8 Samples

Download data: BW

(Submitter supplied) To investigate how HDC1, HDA6, and HDA19 regulate gene transcription and flowering time in long day conditions, we performed RNA deep sequencing (RNA-seq) to compare the transcriptomes of wild type, hdc1, hda6, and hda19 mutants grown in long day conditions.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23157

4 Samples

Download data: BW

(Submitter supplied) To investigate whether the expression of upregulated genes in hdc1 and hda19 is assoiated with histone acetylation levels increased in the hdc1 and hda19 mutants, We carried out ChIP-seq to examine histone H3 acetylation at the whole-genome level.

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17639

4 Samples

Download data: BW

(Submitter supplied) We report the application of ChIP-Seq of H4ac and H3K27me3 histone modifications to jasmonate-treated wild type (DR5) and HDA6 mutant (axe1-5) whole A. thaliana seedlings

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17639

23 Samples

Download data: TXT

(Submitter supplied) To analyze the extent of the overlap between MeJA-induced transcripts and MeJA- induced histone acetylation, the expression profiles of WT untreated (WT), WT+MeJA, axe1-5 untreated and axe1-5+MeJA samples were analysed using the catalog microarray (Agilent design ID:21169). Whole A. thaliana seedlings of axe1-5 mutant and DR5 wild-type lines (Murfett et al 2001) were grown in vitro for 12 days on 1% Murashige and Skoog (MS) medium (Duchefa) supplemented with 1% sucrose, 0.8% phytoagar (Duchefa) and buffered to pH 5.8. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL12621

8 Samples

Download data: TXT

(Submitter supplied) Analysis of the transcriptome of dry hda9-1 mutant seeds with those of Col wild-type seeds, using Affymetrix GeneChip Arabidopsis ATH1 Genome Array. The hda9-1 mutant has reduced primary seed dormancy. We used microarrays to dissect which genes are differentially expressed in the hda9-1 mutant to study the mechanisms how HDA9 affects seed dormancy and germination

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

6 Samples

Download data: CEL

(Submitter supplied) We generated 18 Gb of high-quality sequencing data (~3 Gb per sample) and catalogued the expression profiles of 27,416 annotated Arabidopsis thaliana genes in each sample. The analysis showed differences of transcriptomes between wild-type Col and Nuclear Factor Y (NF-Y) C1,3,4,9 loss of function mutant nf-yc quadruple (nf-ycQ) seedlings treated with 2 days red light. We identified numerous differentially expressed genes that exhibited distinct expression patterns. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

6 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

Platforms:

GPL23157 GPL24025

37 Samples

Download data: BW

(Submitter supplied) Although the Arabidopsis thaliana RPD3-type histone deacetylases have been known to form SIN3 histone deacetylase complexes that are conserved in eukaryotes, it is unknown whether they also form other types of histone deacetylase complexes. Here, we performed affinity purification followed by mass spectrometry and demonstrated that the Arabidopsis RPD3-type histone deacetylases HDA6 and HDA19 can interact with several previously uncharacterized proteins and form three types of plant-specific histone deacetylase complexes, which we named SANT, ESANT, and ARID. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24025

16 Samples

Download data: XLS

(Submitter supplied) Although the Arabidopsis thaliana RPD3-type histone deacetylases have been known to form SIN3 histone deacetylase complexes that are conserved in eukaryotes, it is unknown whether they also form other types of histone deacetylase complexes. Here, we performed affinity purification followed by mass spectrometry and demonstrated that the Arabidopsis RPD3-type histone deacetylases HDA6 and HDA19 can interact with several previously uncharacterized proteins and form three types of plant-specific histone deacetylase complexes, which we named SANT, ESANT, and ARID. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23157

21 Samples

Download data: BW

(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) In eukaryotes, histone acetylation is a major modification on histone N-terminal tails that is tightly connected to transcriptional activation. HDA6 is a histone deacetylase involved in the transcriptional regulation of genes and transposable elements (TEs) in Arabidopsis thaliana. HDA6 has been shown to participate in several complexes in plants, including a conserved SIN3 complex. Here, we uncover a novel protein complex containing HDA6, several Harbinger transposon-derived proteins (HHP1, SANT1, SANT2, SANT3, and SANT4), and MBD domain-containing proteins (MBD1, MBD2, and MBD4). more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

33 Samples

Download data: CSV, TXT

(Submitter supplied) We isolated AtHOS15 as a negative regulator of plant immunity from genetic screen. To investigate how HOS15 influences plant immunity, we performed whole genome transcriptome (RNA-seq) analysis of the hos15-4 mutant. A total of 3,512 differentially expressed genes, with 1,870 upregulated and 1,642 downregulated, were found in hos15-4 mutant compared to wile-type Col-0. Gene Ontology analysis showed that genes involved in defense responses including immune receptor NLR genes are highly enriched among upregulated genes.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19580

6 Samples

Download data: TXT

(Submitter supplied) We found that histone acetylation relays positional information and that a mutant altered in the histone deacetylase (HDAC) gene family member HDA18 exhibits altered H and N epidermal cell patterning. We then performed genome-wide location (ChIP-chip) analyses by using antibody against HDA18 in transgenic HDA18 overexpression Arabidopsis plants. These analyses identified statistically significant enriched DNA associated with HDA18. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10977

1 Sample

Download data: BED, CEL, TXT

(Submitter supplied) To identify salt-resistant related genes by histone deacetylase inhibitor Ky-2, expression profiles between plants treated with or without Ky-2 under salt stress were analyzed using the custom microarray (GPL20781).

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL20781

12 Samples

Download data: TXT